The aim of this study was to investigate epidemiological characteristics of co-infection of HIV and intestinal parasites in a HIV/AIDS highly endemic area in China. A cross-sectional survey was carried out in two villages where HIV/AIDS prevalence in residents was over 1%. Stool samples of all residents in the two targeted villages were examined for the presence of intestinal parasites. Blood examination was performed for the HIV infection detection and anemia test. A questionnaire survey was carried out in all residents participating in the study. A total of 769 individuals were enrolled in the investigation, 720 of whom were involved in stool examination of intestinal parasites. The infection rates of parasites in the residents of the targeted villages were as follows: 0.56% for , 4.03% for Hookworm, 0.28% for , 0.42% for , 21.39% for , 3.89% for , 1.67% for spp., 4.44% for spp., and no infection for . The overall infection rate of intestinal worms was 4.72%, intestinal parasite infection rate was 24.31%, the anemia prevalence rate was 34.68%, the co-infection rate of HIV and intestinal helminthes 2.17%, the co-infection rate of HIV and intestinal protozoa 28.26%, of which the co-infection rates of HIV and , and HIV and spp. were 19.57% and 13.04%, respectively. A significant difference of spp. infection rate was found between HIV-positive group (13.04%) and HIV-negative group (4.70%) (<0.05). Higher prevalence of anemia (34.68%) occurred in the study villages, particularly in children (>50%) and women (>39%). It was concluded that the infection rate of intestinal protozoa in the residents was higher than that of intestinal helminthes in the local setting, and a same pattern appeared in the co-infection rate of HIV and parasites. An interesting finding is that the infection rate of spp. among the HIV-positives was significantly higher than that in the HIV-negatives, and children and women had higher anemia prevalence.