Few studies have focused on the epidemiology of Cryptosporidium in resource-challenged settings in China. We report a community-based cross-sectional study to investigate the prevalence of Cryptosporidium infection and its risk factors and associations with hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) infections. The prevalence of Cryptosporidium infection was 12.6% (95% confidence interval = 11.0-14.3). Individuals living in households with ≥ 5 family members and raising domestic pigs tended to have a greater risk of Cryptosporidium infection. In addition, Cryptosporidium infection was significantly associated with HBV infection. There were no significant associations of Cryptosporidium infection with HIV viral load and HBV viral load. Further studies are needed to determine the association of Cryptosporidium infection with HBV infection.