To determine the endemic status of important human parasite infections in the Eastern Tibet and Western Sichuan Eco-region of Yunnan Province, Shangri-La and Gongshan counties were selected for the survey in 2015 based on The Third National Survey Plan and Implementation of Key Human Parasitic Diseases. The modified Kato-Katz thick Smear Method was used to examine the helminth eggs in the collected fecal samples in duplicate. The species of hookworm was identified by culturing the larvae using filter paper/tubing method from the egg positive fecal samples (one sample one examination) The saline direct smear method and iodine solution smear method were applied to examine protozoa trophozoites and cysts, respectively. The anal transparent tape method was used to detect Enterobius vermicularis and tapeworm infections in children with age of 3-6 years old. Total 1 271 people from 5 villages in Shangri-La and Gongshan counties were enrolled in the survey, 36.0% (458/1 271) of them were infected with one or more of 12 species of helminths and protozoa. Among them the infection rate was 31.9%（406/1 271） for 5 species of helminth and 5.9% for 7 species of protozoa. The prevalence of soil-transmitted helminths (STH) was 31.9% with Trichuris trichiura as the most common STH (23.1%). The prevalence of STH in Gongshan (50.0%, 383/764) was significant higher than that in Shangri-La (4.5%, 23/507) （P < 0.05). Among the STH infections, most of them were light infection (78.7%, 509/647), with less medium infection (19.3%, 125/647) and heavy infection (2.0%, 13/647). The overall prevalence of protozoan infections was 5.9% in investigated people with Blastocystis hominis as the most common protozoan infection (2.2%). The prevalence of protozoan infections in Shangri-La (10.1%, 51/507） was significantly higher than that in Gongshan (3.1%, 24/764）(P < 0.05）. There was no significant difference in the prevalence of intestinal parasite infections between male (36.3%, 206/567） and female (35.8%, 252/704） participants (P > 0.05). Children with age of 0-9 years old had the highest prevalence of intestinal parasite infections (50.0%, 95/190）. Regarding education level, people with high school or professional school had the highest prevalence of intestinal helminth and protozoa infections (41.2%, 14/34）. In terms of ethical nationality, Dulong people had the highest prevalence of intestinal parasite infections (84.0%, 225/268）. There was significant differences in the prevalence of intestinal parasite infections among people with different age, occupations, education levels and ethical nationalities（P < 0.05）.The survey results showed that the prevalence of key human intestinal parasite infections is still high in the Shangri-La and Gongshan Counties within Eastern Tibet and Western Sichuan Eco-region of Yunnan Province. It is necessary to strengthen the prevention, control and surveillance measures for intestinal parasitic diseases in farmers, students and children who have the highest infections.