Objective To understand the endemic status of echinococcosis in Yunnan province so as to provide evidence basis for the better prevention and control of the disease. Methods Based on the National Hydatid Disease Epidemiological Investigation Program, epidemiological investigation of echinococcosis was performed in Deqin, Eryuan, Weixi and Shangri-La counties from 2012 to 2015, and in other 24 counties (Binchuan, Daguan, Dayao, Deqin, Eryuan, Fugong, Gongshan, Gucheng, Heqing, Huize, Jianchuan, Lanping, Longyang, Lushui, Mouding, Shilin, Tengchong, Weixi, Shangri-La, Xuanwei, Yangbi, Yulong, Yunlong and Zhaoyang) from 2016 to 2017. Three townships from each county and 4 villages from each township were selected as investigation sites based on cluster random sampling method. Residents with age over 1 year old were examined by abdominal ultrasonography in 2012, 2016 and 2017. The diagnosis of hydatid disease was made based on the ultrasonic imaging combining with epidemiological history, clinical manifestations and serological test for those suspected. During the investigation from 2013 to 2015, residents with age over 1 year old and all students from one primary school in each county were chosen for testing anti-Echinococcosus IgG antibody in their sera. Those with antibody positive were further examined by abdomanal ultrasonography to confirm the diagnosis. A questionnaire investigation was carried out in enrolled participants for the awareness of infection and prevention of hydatid disease. Each dog was selected from 20 households in each village for detecting the coproantigen of Echinococcus by ELISA. In each county (city), visceral organs were collected from locally raised sheep/pigs (100) or cattle (500) for examining hydatid cysts by necropsy. All data were statistically analyzed using SPSS 17.0 software. Results A total of 768 villages were investigated including 192 villages in 4 counties from 2012 to 2015 and 576 villages in 24 counties from 2016 to 2017. A total of 105 555 residents were examined by ultrasound, of whom 67 (0.06%) were detected with hydatid disease, all infected with Echinococcus granulosus. The prevalence of cystic echinococcosis in the investigated population in 2012, 2016 and 2017 were 0.05% (4/7 512), 0.05% (32/61 110) and 0.08% (31/36 933), respectively. Among the different investigated countries, the prevalence > 0.10% was distributed in Heqing (0.19%, 7/3 779), Shilin (0.17%, 8/4 799), Zhaoyang (0.16%, 4/2 520), Dayao (0.12%, 4/3 378), Eryuan (0.11%, 11/9 738), Yunlong (0.11%, 5/4 465) and Jianchuan (0.11%, 5/4 595). The prevalence of cystic echinococcosis in males and females were 0.05% (23/46 179) and 0.07% (44/59 376), respectively (P > 0.05). The prevalence increased with age (χ² = 21.414, P < 0.05), with highest in group of 60-79 years old (0.12%, 26/22 724) followed by people with age over 80s (0.08%, 2/2 414). There was a significant difference in prevalence among the different occupations (χ² = 11.581, P < 0.05), with highest prevalence in farmers and herdsmen (0.08%, 64/82 978). As to the education level, the prevalence was highest in the people with illiteracy (0.11%, 26/22 724) with significant difference compared to people with higher educational levels (χ² = 16.307, P < 0.05). The overall dog coproantigen positive rate was 4.87% (965/19 812), The dog positive rate > 5% was located in Longyang District (8.41%), Shangri-La City (8.13%), Lushui County (7.21%), Eryuan County (7.50%), Fugong County (6.54%) and Muding County (5.18%), with statistical difference among different counties(χ² = 69.287, P < 0.05). From 2012-2017, the average dog coproantigen positive rates in these investigated sites was 1.24% (16/1 293), 13.41% (483/3 601), 5.10% (95/1 862), 3.01% (72/2 389), 1.56% (103/6 588) and 4.81% (196/4 079), respectively. The overall hydatid detection rate in livestock (sheep, cattle and pigs) was 0.12% （32/27 502）, with 1.49% (2/134) in 2015, 0.21% (8/3871) in 2016 and 0.10% (22/21 125) in 2017. The overall awareness rate for echinococcosis among the investigated population was 52.39% (9 974/19 039), 47.72% (607/1 272), 51.77% (789/1 524), 61.00% (549/900), 77.20% (772/1 000), 43.50% (5 075/11 668) and 81.57% (2 182/2 675) from 2012 to 2017, respectively. Conclusion Echinococcosis in Yunnan Province showed a low and medium prevalence, all of which were infected with E. granulosus. Farmers and herdsmen over 40 years old with low educational level had the highest infection rate.