Objective To investigate the epidemiology of echinococcosis in Inner Mongolia Autonomous Region, so as to provide insights into echinococcosis control. Methods Baseline surveys on the epidemiology of echinococcosis were performed using a stratified cluster sampling method in 36 banners (counties, cities, districts) across 11 leagues (cities) in Inner Mongolia Autonomous Region from 2012 to 2018. Approximately 3 200 residents were recruited in each banner (county, city, district), and human echinococcosis was diagnosed with ultrasound. Fecal samples were randomly collected from one dog per household in the surveyed villages, and the Echinococcus coproantigen was detected using ELISA in dogs. In addition, Echinococcus infection was identified using necropsy in livestock (sheep). Results Echinococcosis patients were diagnosed in 22 banners (counties, cities, districts), including 15 in pastoral areas, 5 in semi-agricultural and semi-pastoral areas, and 2 in agricultural areas. The highest number of echinococcosis cases was recorded in Xiwuzhumuqin Banner (16 cases, 21.6% of all cases), and there were 6 banners (counties, cities, districts) with echinococcosis prevalence of 0.10% to 0.50%, and 16 with prevalence of 0.03% to 0.10%. A total of 115 155 residents received ultrasound screening for echinococcosis, and 74 residents were diagnosed with echinococcosis (all cystic echinococcosis), with a prevalence rate of 0.11% (74/115 155). Women (0.08% prevalence, 51/60 544), residents at ages of 30 to 59 years (accounting for 60.81%, 45/74), herders (accounting for 55.41%, 41/74), residents with an educational level of primary school (0.10% prevalence, 39/39 237), and nomadic populations (0.29% prevalence, 6/2 097) were identified at a high risk of echinococcosis. A total of 17 909 dog feces samples were collected from 36 banners (counties, cities, districts), and the positive rate of Echinococcus coproantigen was 1.84% (330/17 909) in dogs. Dog feces positive for Echinococcus coproantigen was detected in 26 banners (counties, cities, districts), and there was one banner with a 5.00% and higher positive rate of Echinococcus coproantigen in dogs (New Barag Right Banner, 11.75%), 18 banners (counties, cities, districts) with positive rates of 1.00% to 5.00% and 8 banners (counties, cities, districts) with positive rates of 0.29% to 1.00%. A total of 32 100 sheep were examined for echinococcosis in 33 banners (counties, cities, districts), and the prevalence of echinococcosis was 0.46%. Sheep with echinococcosis were found in 14 banners (counties, cities, districts), with echinococcosis prevalence of 0.10% to 7.30%, and there were 3 banners (counties, cities, districts) with echinococcosis prevalence of > 1.00%, all in pastoral areas. Conclusion Echinococcosis is widely but overall lowly prevalent in Inner Mongolia, and there are obvious regional and population clustering distributions. Intensified echinococcosis prevention and control is recommended in key areas and populations.