Objective To investigate the current status of human intestinal protozoa infections in Jiangxi Province, so as to provide the evidence for the formulation of prevention and control measures. Methods A survey was performed in 2014 according to the Protocol of the 3rd National Survey on the Status of Human Key Parasitic Infections combining with the specific economic and geographic situation in Jiangxi Province. Total 84 survey sites were chosen from 28 counties (cities and districts) using stratified cluster sampling method based on the different geographic zones. No less than 250 permanent residents with no more than 1/3 of children with age less than 12 years old were recruited in the survey in each site. The fecal samples were collected from each participant. The infected protozoan cysts were examined using iodine staining and the trophozoites were examined using direct saline smear under microscope. Each fecal sample was examined once and the statistical analysis was performed using IBM SPSS Statistics 20 and chi-square test. Results A total of 21 569 people were participated in this survey. The overall prevalence of protozoa infections was 1.4% (307/21 569) with eight species of intestinal protozoa identified. Specifically the prevalence of Entamoeba histolytica was 0.2% (45/21 569), E. coli 0.5% (104/21 569), Gardia lamblia 0.1% (26/21 569), Blastocystis hominis 0.3% (68/21 569), E. hartmani 0.1% (28/21 569) and Endolimax nana 0.2% (46/21 569). Three cases of Iodamoeba butschlii and 1 case of Balantidium coli were identified. The prevalence of protozoa infections was highest in Nanling hilly areas (2.8%, 132/4 742) with B. hominis and E. nana as dominant infected species. The lowest prevalence of protozoa infections was identified in Zhejiang/Fujian hilly areas(0.3%, 18/5 887). There was significant difference in the prevalence of intestinal protozoa infections among different ecological areas(P < 0.01). The largest number of cases of E. histolytica infection was found in Jiujiang City, accounting for 93.3% (42/45) of the total cases in the province. E. coli and G. lamblia infections were common in Yichun City, accounting for 65.4% (68/104) and 46.2% (12/26) of the total cases in the province, respectively. The 1 case of B. coli infection was also found in Yichun City. The infections of B. hominis, E. hartmani and E. nana were mostly found in Ganzhou City, accounting for 69.1% (47/68), 82.1% (23/28) and 97.8% (45/46) of the total cases in the province, respectively. There were 12 cases of mixed protozoa infections identified province-wide. There was no significant difference in the prevalence of intestinal protozoa infections between male (1.4%, 148/10 582) and female (1.5%, 159/10 987) (P > 0.05). The highest prevalence of intestinal protozoa was observed in children with age 0-9 years old (2.0%, 64/3 243), and the lowest in the elders with age above 70 (0.9%, 16/1 710), however, there was no statistical significance among different age groups (P > 0.05). In different occupation groups, the highest prevalence of intestinal protozoa infections was found in workers and businessmen(1.8%, 6/329) and the lowest in teachers and retirees (0.8%, 2/248). There was no significant difference in the prevalence among different occupations (P > 0.05) though. In different level of education, the highest prevalence was identified in population with low education (illiterate, 1.5%, 56/3 635) and the lowest in people with high education (college and above, 0.2%, 1/219), but without statistical difference in people with different educational levels (P > 0.05). The prevalence of intestinal protozoa infections in the high income areas was 1.3% (102/7 837) with E. coli as a dominant infected species. The protozoa infection in people with medium income was 0.9% (50/5 456) mainly with E. histolytica and G. lamblia infected. The infection rate in people with low income was 1.9% (155/8 276), mainly with B. hominis and other protozoans. The prevalence of intestinal protozoa infections was significant difference between people with different economic level (P < 0.01). Conclusion The overall prevalence of human intestinal protozoa infections in Jiangxi Province is low, but more serious in the population in Nanling hilly areas with lower economic level. More control measures should be performed in this part of population.