Objective To investigate current endemic status of common human parasite infections in Fujian Province in order to provide scientific basis for formulating better prevention and control measures. Methods Based on the Third National Survey Plan for Common Human Parasites, the survey sites were selected by using stratified cluster random sampling method in 2015. Not less than 250 permanent residents over 3 years old were enrolled in each site. The fecal samples were collected from each participant and the helminthic eggs were examined under microscope using Kato-Katz thick smear method in duplicate. The cysts and trophozoites of intestinal protozoa were examined using direct saline smear and iodine staining. Results Total 41 survey sites were selected for soil-transmitted helminth (STH) infections, 75 sites selected for intestinal protozoa infections from 15 counties. For survey of Clonorchis sinensis infection, total 12 sites were selected from 7 cites (urban) and 10 sites selected from 5 towns (suburban). A total of 16 799 residents from 138 survey sites from 27 counties (9 prefectures) were examined, and the overall prevalence of all parasite infection was 3.69% (618/16 799). For STH infections, totally 10 652 residents were examined with overall prevalence of 3.67% (391/10 652) identified. Three STH have been identified with individual prevalence for Ascaris lumbricoides 0.06% (7/10 652), hookworms 3.36% (358/10 652) and Trichuris trichiura 0.27% (29/10 652). For intestinal protozoan infections, a total of 10 652 residents were examined and the overall prevalence was 2.08% (222/10 652), with individual prevalence for Blastocystis hominis 0.79% (85/10 652), Endolimax nana 0.58% (62/10 652), Entamoeba coli 0.41% (44/10 652), E. hartmanni 0.18% (19/10 652), E. polecki 0.09% (10/10 652), and Giardia lamblia 0.02% (2/10 652). For C. sinensis infections, total 6 147 residents were examined with over prevalence of 0.09% (6/6 147), 2 of them were identified in urban areas (0.05%, 2/3 418) and 4 identified in suburban areas (0.15%, 4/2 729）. There is no statistical difference for the prevalence of C. sinensis infection identified in urban and suburban regions (P > 0.05). For STH infection, there was no significant difference in the prevalence between male (3.31%) and females (4.01%) (P > 0.05). People with 65-years old or above had the highest prevalence of 7.87%, and people with age less than 15 years old had the lowest prevalence (0.38%), with significant difference for the distribution of STH infections in different groups of age (P < 0.01). Famers had the highest prevalence of 4.63% compared to people with other occupations (P < 0.01). People with low education (primary school or less) had the highest prevalence of STH infection (4.85%) and people with high education (university or above) had the lowest prevalence (1.29%), with significant difference compared with people with different education levels (P < 0.01). Among the 15 counties investigated, the prevalence of STH was highest in Ninghua (16.59%) and lowest in Zhouning (0). Among the 9 prefectures investigated, the highest prevalence of STH was observed in Sanming (8.87%) and lowest in Ningde (0.19%). Compared with different ecological zones, people living in Fujian/Zhejiang mountain zone had higher prevalence of STH (4.12%, 226/5 480) than people living in Yunnan/Guizhou/Guangdong/South Fujian ecological zone (3.19%, 165/5 172), with statistical difference (P < 0.05). Compared to the prevalence of STH identified at the first survey (95.65%) and the second survey (89.85%), the prevalence of STH identified at current survey has dropped 95.65% and 89.85%, respectively. Conclusion The total prevalence of human common parasite infections is greatly reduced in Fujian Province identified in this survey, and has fallen down to its lowest level in history. Among STH, hookworm infection still needs to be better controlled.