Objective To estimate the overall economic burden of echinococcosis patients in Xinjiang from 2014 to 2023 and to identify its influencing factors, so as to provide the scientific evidence for formulation and improvements of medical control strategies for echinococcosis in Xinjiang. Methods A total of 8 hospitals were sampled from Xinjiang by means of stratified sampling and convenience sampling, including 4 Class Ⅲ Grade A hospitals and 4 Class Ⅱ Grade A hospitals. Medical records were collected from hospitalized patients with a primary diagnosis of echinococcosis from January 1, 2014 to December 31, 2023, and variables were retrieved from medical records, including gender, age, ethnicity, length of hospital stay, hospitalization cost, hospital level, region, surgical treatment, health insurance status, and type of echinococcosis. Subjects’ demographics and cost distribution were analyzed with descriptive statistics. Univariate analysis was performed with Mann-Whitney U test and Kruskal-Wallis H test, and independent factors affecting hospitalization costs were identified using a logarithmic multiple linear regression model (stepwise method). Indirect economic burden was calculated with disability-adjusted life year (DALY) combined with the human capital method using the following formula: indirect economic burden = gross national product per capita × DALY × productivity weight. SPSS 24.0 was used for statistical analyses. Results A total of 5 184 hospitalized patients with echinococcosis were included. The number of patients discharging from hospital peaked in 2017 (865 cases), dropped to the lowest in 2022 (230 cases, a decrease of 73.4% compared with the peak), and rebounded to 361 cases in 2023. The subjects had a median age of 44 years, and were primarily at ages of 45 to 59 years (32.9%, 1 703 cases). Of all subjects, 54.5% (2 823 cases) were men, and 90.1% (4 670 cases) suffered from cystic echinococcosis. Hospitalization costs showed a skewed distribution, with the median increasing from 23 137.2 Yuan in 2014 to 34 921.0 Yuan in 2022. The mean hospitalization cost was higher for alveolar echinococcosis patients (71 302.7 Yuan) than for cystic echinococcosis patients (29 397.3 Yuan; Z = -11.750, P < 0.05), and the mean hospitalization cost was higher among patients from northern Xinjiang (36 283.3 Yuan) was higher than those from southern Xinjiang (17 703.7 Yuan)(Z = -19.701, P < 0.05). The highest mean cost was seen among patients with length of hospital stay exceeding 30 days (106 761.4 Yuan; H = 1 263.033, P < 0.05). Logarithmic multiple linear regression analysis identified length of hospital stay (β = 0.414), surgical treatment (β = ‒0.471), hospital level (β = 0.210), region, type of echinococcosis, age, and health insurance status as independent factors affecting hospitalization costs (adjusted R² = 0.553, P < 0.05). Indirect economic burden analysis showed that echinococcosis caused a total of 10 007.3 DALYs lost during the study period, with an mean loss of 2.0 DALYs per patient. Patients at ages of 15 to 44 years had the highest disease burden, with a total DALY loss of 5 465.0 person-years, accounting for 54.6% of the total loss. The total indirect economic burden was 423.823 million Yuan, with a mean indirect economic burden of 82 000 Yuan per patient. Conclusion The economic burden of echinococcosis patients shows significant structural differences in Xinjiang. Alveolar echinococcosis is the core disease type leading to high medical costs, and its resource consumption pattern is essentially different from that of cystic echinococcosis. Young and middle-aged populations at ages of 15 to 44 years have more than half of the productivity loss and is the main population affected by indirect economic burdens.