Toxoplasma gondii is an important zoonotic parasite that can infect almost all warm-blooded animals, including humans, and infection may result in many adverse effects on animal husbandry production. Animal husbandry in Inner Mongolia is well developed, but data on T. gondii infection in sheep are lacking. In this study, we determined the seroprevalence and risk factors associated with the seroprevalence of T. gondii using an indirect enzyme-linked immunosorbent assay (ELISA) test. A total of 1853 serum samples were collected from 29 counties of Xilin Gol League (n = 624), Hohhot City (n = 225), Ordos City (n = 158), Wulanchabu City (n = 144), Bayan Nur City (n = 114) and Hulunbeir City (n = 588). The overall seroprevalence of T. gondii was 15.43%. Risk factor analysis showed that seroprevalence was higher in sheep ≥12 months of age (21.85%) than that in sheep <12 months of age (10.20%) (p < 0.01). Seroprevalence was higher in male sheep (18.76%) than females (12.80%) (p < 0.01). Barn-feeding sheep (23.13%) had higher prevalence than grazing sheep (10.94%) (p < 0.01). The seroprevalence was significantly different in different districts (p < 0.01). This study shows that sheep are exposed to T. gondii in Inner Mongolia, and provides a data reference for public health and disease control.