Background: Cryptosporidium spp. is an important intestinal protozoan causing diarrhea in humans, livestock, and wild animals. Cryptosporidium infection remains a major public health issue, but its epidemiology in humans is still unclear, particularly in rural China. This study was designed to determine the prevalence of and risk factors associated with Cryptosporidium infection in a rural southwestern Chinese community. Methods: A community-based cross-sectional survey was conducted among 687 residents of a small town in a Yi autonomous prefecture of southwest China in 2014. Blood samples were examined using a broad set of quality-controlled diagnostic methods for hepatitis B virus (HBV) and human immunodeficiency virus (HIV). Stool specimens were processed using the modified acid-fast staining method, and microscopically examined for Cryptosporidium infection. Univariable and multivariable analyses were performed to determine the risk factors associated with Cryptosporidium infection. Results: The majority of the participants were Yi people with poor living conditions and unsatisfactory hygiene habits, and the study area was of very low socioeconomic status. Of the 615 individuals included in the analysis, 14 (2.3%) were HIV positive, 51 (8.3%) were infected with HBV, and 74 (12.0%) had Cryptosporidium infection. The prevalences of HIV/HBV, HIV/Cryptosporidium, and HBV/Cryptosporidium co-infections were 0.3%, 0.3%, and 1.8%, respectively. The prevalence of HBV infection was higher in individuals with Cryptosporidium infection (chi(2) = 5.00, P = 0.03). Owning livestock or poultry was an important risk factor for Cryptosporidium infection (aOR = 2.27, 95% CI: 1.01-5.08, P < 0.05). Cryptosporidium infection was significantly associated with HBV infection (aOR = 3.42, 95% CI: 1.47-7.92, P < 0.01), but not with HIV infection (aOR = 0.57, 95% CI: 0.07-4.39, P = 0.59). Conclusions: The prevalence of Cryptosporidium infection was high in the rural area of southwestern China that was investigated, and there was a significant association between HBV infection and Cryptosporidium infection. Further investigations are needed to determine the significance of Cryptosporidium infection in patients infected with HBV.