Whilst infections with soil-transmitted helminths are common across China, the public-health significance of Schistosoma japonicum and food-borne helminths is more focalized. Only few studies have investigated the local epidemiology of helminth infections in rural China, including risk factor analysis. We collected stool and blood samples from 3220 individuals, aged 5-88 years, from 35 randomly selected villages in Eryuan county, Yunnan province, China. Stool samples were subjected to the Kato-Katz technique and examined for helminth eggs. Blood samples were tested for Trichinella spp., S. japonicum and cysticerci-specific antibodies. Data on individual and family-level risk factors were collected using questionnaires. The prevalence of Ascaris lumbricoides, Taenia spp., Trichuris trichiura and hookworms was 15.4%, 3.5%, 1.7% and 0.3%, respectively. The seroprevalence of Trichinella spp. was 58.8% and that of cysticercosis 18.5%. The egg positivity rate of S. japonicum in the 13 known endemic villages was 2.7%, and the corresponding seroprevalence was 49.5%. We observed a strong spatial heterogeneity in the families' economic status. S. japonicum infections were more prevalent among the Han than Bai nationality (odds ratio (OR)=3.77, 95% confidence interval (CI)=1.97-7.23) and tobacco growers (OR=3.66, 95% CI=1.77-7.60) and was only found at elevations below 2150 m above sea level. A. lumbricoides and Taenia spp. infections were more prevalent at altitudes above 2150 m when compared to lower settings (OR=1.51, 95% CI=1.24-1.84 and OR=5.32, 95% CI=3.42-8.28, respectively). The opposite was found for T. trichiura (OR=0.31, 95% CI=0.14-0.70). Our findings can guide the design and spatial targeting of control interventions against helminth infections in Eryuan county.