Objective To investigate the hospitalization expenses of patients with cystic echinococcosis undergoing surgery in Ningxia for providing reference basis to reduce the economic burden hospitalized patients. Methods Data from patients who underwent cystic echinococcosis surgery from 2016 to 2021 in Ningxia were collected, including the patient’s basic information, the number of hospitalisation days and the cost of surgery and other information. SPSS 20.0 statistical software was used for statistical analysis. The average hospitalization cost was expressed in median per capita. Z test and F test were used for comparison among groups. The hospitalization expense was assigned as dependent variable. The surgery year, gender, age, occupation, education level, number of operations, hospital grade, the time interval from diagnosis to operation and the days staying in hospital were taken as independent variables for multiple linear logistic regression analysis. Result A total of 486 patients’ information undergoing surgery were collected, of them the total hospital cost, average cost per patient and the median cost was 11.391 million yuan, 23 438.7 yuan, and 20 362.5 yuan. Hospitalization expense mainly include 17 categories, the top 3 median expenses were drug fee (8 030.0 yuan), consumble material fee (5 000.0 yuan) and operation fee (3 436.4 yuan). The median hospitalization expenses of men and women were 20 126.1 yuan and 20 931.4 yuan, respectively, with no significant difference (Z = -0.552, P > 0.05). The median hospitalization expenses of patients aged 40-59 years was the highest, which was 20 835.5 yuan. The difference of hospitalization expenses among different age groups was statistically significant (Z = 8.2, P < 0.05). Among different occupational patients, the median hospitalization expense of other occupational patients was the highest, which was 22 655.0 yuan. There was no statistically significant difference in hospitalization expense of different occupational patients (Z = 1.838, P > 0.05). The median hospitalization expenses of illiterate patients was the highest, which was 23 286.4 yuan. There was no statistically significant difference in hospitalization expenses of patients with different education levels (Z = 6.729, P > 0.05). The hospitalisation cost of patients with a time interval of more than 1 year from diagnosis to surgery (20 830.1 yuan) was higher than that of patients with an interval of ≤ 1 year (19 127.0 yuan) (Z = -2.121, P < 0.05). From 2016 to 2021, the hospitalization expense of patients with one operation (20 274.3 yuan) is lower than that of patients with multiple operations (20 963.0 yuan) (Z = -2.079, P < 0.05). The median hospitalization expense of patients with hospitalization time ≤ 21 days (19 768.9 yuan) was lower than that of patients with hospitalization time > 21 days (30 732.0 yuan) (Z = 9 069.5, P < 0.01). There was no statistically significant difference between the median hospitalization expenses of patients with medical insurance (20 313.0 yuan) and those without medical insurance (29 798.5 yuan) (Z = -1.392, P > 0.05). The median hospitalization cost of patients undergoing hepatectomy was the highest (31 640.5 yuan), and the median hospitalization cost of patients undergoing different surgical methods was statistically significant (Z = 22.174, P < 0.01). From 2016 to 2021, the median hospitalization expense increased from 17 689.5 yuan to 27 090.0 yuan (Z = 27.560, P < 0.01). The median hospitalization expenses of provincial, municipal and county hospitals were 26 227.0 yuan, 16 979.0 yuan and 12 988.1 yuan, respectively. The median hospitalization expenses decreased with the decline of hospital level (Z = 146.875, P < 0.01). The average days staying in provincial and municipal hospitals is 14 days, and that in county-level hospitals is 15 days. There was a statistically significant difference in the number of days staying in hospitals of different levels (F = 9.594, P < 0.05). Multivariate logistic regression analysis showed that four factors, including operation mode, hospital level, days staying in hospital and operation year, were related to hospitalization expenses (P < 0.05). Among 486 patients, the total subsidy of the national echinococcosis project, the average cost per person and the median cost per person were 2 732 224.6 yuan, 5 621.9 yuan and 6 000.0 yuan. The total, the average capita and median of out-of-pocket expenses for each patient were 1 864 120.1 yuan, 8 176.0 yuan and 6 169.0 yuan respectively. After medical insurance and national hydatid disease project subsidies, the majority had no out-of-pocket payment accounting for 53.1% (258/486), followed by 15.2% (74/486) paid 1 000-4 999 yuan out-of-pocket and 15.2% (74/486) paid 5 000-9 999 yuan out-of-pocket. The percentage of patients with no out-of-pocket fee increased from 41.7% (45/108) in 2016 to 63.6% (35/55) in 2020 and decreased to 35.9% (23/64) in 2021. Conclusion From 2016 to 2021, the median hospitalization expenses of patients for surgery on cystic echinococcosis in Ningxia increased year by year, while the proportion of patients with no out-of-pocket fees increased year by year, but decreased to 35.9% in 2021. It is suggested that the subsidy standard of the hydatid disease prevention and control project should be appropriately raised, and patients are encouraged to choose a nearby designated hospital for treatment, so as to reduce the hospitalization costs.