According to the guidelines of the Scheme and Implementation Guideline of Nationwide Survey on Human Major Parasitic Diseases in China, five survey sites were selected from 3 counties (city) in the ecological region of southern part of Yunnan-Guangxi-Guangdong (Y-Gx-Gd) neighboring area in Yunnan Province in 2015 using the stratified cluster random sampling method. At least 250 local residents at ages of over 3 years were surveyed in each survey site. Intestinal helminth eggs were examined using the modified Kato-Katz thick-smear method (two slide-reading/sample); hookworm species was identified using the tube filter paper culture technique; Enterobius vermicularis eggs were examined using additional the transparent adhesive tape method for children at ages of 3 to 6 years; and trophozoites or cysts of intestinal protozoa were detected using direct smear method with physiological saline-iodine. All data were processed using the statistical software SPSS version 17.0. A total of 1 278 residents in the five survey sites were examined, among them 350 were found positive of intestinal parasites infection, with an overall infection rate of 27.4%. Totally, 10 parasite species were identified, including 5 species of helminths and protozoa, respectively. Of the 350 positives, 302 were infected with soil-transmitted nematodes (infection rate 23.6%), 64 infected with protozoa (infection rate 5.0%) and 5 infected with Taenia (infection rate 0.4%). The difference of infection rate between different parasite species was statistically significant (χ² = 464.56, P < 0.01). The infection rate of intestinal parasite was 26.5% (165/622) in men and 28.2% (185/656) in women, showing no significant difference between genders (χ² = 0.450, P > 0.05). There was no significant difference of infection rate between intestinal parasite, soil-transmitted nematode, and intestinal protozoa in different genders (χ² = 0.450, 0.510, 0.001, P > 0.05). The distribution of ethnicity, education levels and age groups in infection rate of intestinal parasite indicated that the highest was seen in the residents of Miao ethnicity (45.3%, 115/254), illiterate (33.2%, 92/277) and the age group of 6—69 years (42.4%, 56/132). Difference in infection rate of intestinal parasite and soil-transmitted nematode between different ethnicities, education levels and age groups was statistically significant (χ² = 72.75 and 78.01, 15.74 and 18.60, 50.74 and 55.57, P < 0.01), but not significant in intestinal protozoa infection (χ² = 5.54, 1.93 and 12.78, P > 0.05). Soil-transmitted nematode infection in the residents was largely mild, as such that the mild infection of Ascaris, Trichuris and hookworm accounted for 66.7% (42/63), 98.3% (58/59) and 96.8% (212/219), respectively. Intestinal parasite infection was detected in all three counties, with the highest infection rate of soil-transmitted nematode found in Hekou County (32.0%, 160/516) (χ² = 32.38, P < 0.05). The infection rate of soil-transmitted nematode was 5.7% (29/505) in Malipo County, 4.7% (24/516) in Hekou County and 4.3% (11/257) in Yingjiang County, with no significant difference between the three counties surveyed (χ² = 0.997, P > 0.05). The survey indicates that the infection rates of intestinal parasite and hook worm remain considerably high, while the infection rate of intestinal protozoa is low in the ecoregion of the southern part of Y-Gx-Gd neighboring area of Yunnan Province.