Objective To understand the current status of human intestinal protozoan infections in Sichuan Province. Methods An epidemiological survey was carried out in Sichuan Province according to the Protocol of National Survey Scheme on Major Human Parasitic Diseases from April to June, 2015. Total 45 survey sites were selected from 15 counties (cities and districts) within 5 ecological zones of Sichuan by using a stratified sampling method. No less than 250 rural permanent villagers in each site were enrolled in the survey and the fecal sample was collected from each participant. The protozoan cysts in the feces were examined by Lugol’s iodine staining method(one check for each sample). The protozoan trophozoites were examined only in the fresh diarrheal or bloody fecal samples using saline direct smear method(one check for each sample). Each fecal sample was examined once. SPSS 23.0 software was used for statistical analysis. The prevalence difference among the different groups of people was compared by χ² test. Results Total 11 403 people were investigated. The overall prevalence of intestinal protozoan infections was 2.0% (223/11 403) province-wide. Total 9 protozoan species were identified in infected people including Entamoeba histolytica (0.2%, 22/11 403), E. coli (0.7%, 78/11 403), Gardia lamblia (0.1%, 9/11 403）, Blastocystis hominis (0.5%, 60/11 403）, E. hartmani (0.2%, 17/11 403）and Endolimax nana(0.6%, 67/11 403). Two cases of Balantidium coli, one case of each Iodamoeba butschlii and Embadomonas intestinalis were identified. The highest prevalence of intestinal protozoan infections was identified in areas of Source of rivers-Southern Gansu ecological zone (6.5%, 148/2 278),and the lowest prevalence was identified in Sichuan basin zone (0.4%, 10/2 289). There was a significant difference in the prevalence of protozoan infections among different ecological zones (P < 0.01). The highest prevalence of intestinal protozoan infections was identified in Markam County (10.2%, 102/1 001), followed by Ganzi County (6.1%, 46/755). There was significant difference in the prevalence of intestinal protozoa among different counties (cities and districts) (P < 0.01). The prevalence of intestinal protozoa in males and females were 1.9% (97/5 247) and 2.1% (126/6 156), respectively, without significant difference (P > 0.05). People with age 20-29 had the highest prevalence of intestinal protozoa and no protozoa infection was found in people with age of 80 or older, however, there was no significant difference in the prevalence of intestinal protozoa among different age groups (P > 0.05). Regarding the education, people with no education (illiteracy) had the highest prevalence (3.2%, 73/2 317) and no infection was identified in people with education of college and above, with significant difference among people with different education(P < 0.01). In terms of occupation, the highest prevalence of protozoan infections occurred in herdsmen (4.8%, 20/421) followed by students (2.0%, 30/1 491), however, there was no significant difference in the prevalence among different occupations (P > 0.05). In terms of ethnic groups, the highest prevalence was found in Tibetan population (5.3%, 149/2 381) followed by Han population (0.9%, 74/7 857) with significant difference in the prevalence of protozoan infections among different nationalities (P < 0.01). Conclusion Source of rivers Gannan ecological zone and Markam County kept relatively high prevalence of protozoan infections in which more prevention and control measures should be adopted. The people with low education and Tibetan are the main population for the control of intestinal protozoan infections.