Objective To understand the endemic status of major human intestinal parasites in rural areas of Shandong Province, so as to provide scientific evidence for formulating prevention and control measures. Methods The survey was conducted based on the National Survey Plan and Implementation for Human Key Parasitic Diseases from 2014 to 2015. Total 52 pilot study sites were selected using a stratified cluster random sampling method based on different ecologic and geographic status, economic levels, each site with at least 250 residents enrolled. Fecal samples were collected from all participants and the intestinal helminth eggs in the feces were examined under microscope using Kato-Katz thick smear method. The direct smear method was used to detect intestinal protozoan trophozoites and cysts. The adhesive tape method was used to detect pinworm eggs around anal in children aged 3 to 6. The information for the natural factors, toilet, drinking water and diet and hygiene behaviors were collected for analyzing risks of infections. The difference in infection rates was statistically analyzed by chi-square or Fisher exact test using SPSS 18.0. Results A total of 13 620 people were investigated and the overall intestinal parasite infection rate was 1.06% (144/13 620), among them the intestinal helminth infection rate was 0.87% (118/13 620) and the intestinal protozoa infection rate was 0.19% (26/13 620). The pinworm infection rate in children with age of 3-6 was 1.71% (15/877). Total 5 species of intestinal helminthes and 3 species of intestinal protozoa were identified. The top three intestinal helminths were Trichuris trichiura (0.58%, 79/13 620), Ascaris lumbricoides (0.16%, 22/13 620) and Enterobius vermicularis (0.12%, 17/13 620). Among 118 helminth infecton cases, 4(3.39%) cases were mixed infection, and which were all mixed with Trichuris trichiura and Ascaris lumbricoides, while 26 protozoa infection cases were all single infection. Among 22 Ascaris lumbricoides infection cases, 20(90.91%) cases were mild infection, 1 (4.55%) case was moderate infection and 1 (4.55%) case was severe infection. 3 Ancylostoma sp. infection cases were all mild infection. Among 79 Trichuris trichiura infection cases, 70(88.61%) were mild infection, 8 (10.13%) were moderate infection and 1 (1.27%) case was severe infection. 1 Clonorchis sinensis infection case was mild infection. The top three counties with highest intestinal parasite infection rate were Rushan, Weihai (8.23%, 65/790); Mengyin, Linyi (1.51%, 16/1 063) and Yanggu, Liaocheng (1.26%, 10/793). The intestinal parasite infection rates in population between two ecologic zones were significantly different, with 0.61% in plain ecologic zone and 1.50% in hilly ecologic zone (P < 0.01). The pinworm infection rate was significantly higher in plain zone (0.21%) than in hilly zone (0.04%), while T. trichiura infection rate was significantly higher in hilly zone (1.13%) than in plain zone (0.01%) (P < 0.01). There was no significant difference in intestinal parasite infection between male (0.90%) and female (1.20%) (P > 0.05). The infection rate in old people with age of 70-79 (2.30%) was higher than other age groups with statistical difference (P < 0.01). There was no significant difference in infection rate in population with different occupations or different education even though the prevalence of intestinal parasites was high in preschool children (1.49%) (P > 0.05). Drinking water source was a risky factor, people drinking water from well had higher infection rate of intestinal parasites (1.88%) than people drinking tape water (0.82%) or spring water (0.37%) (P < 0.01). People eating raw vegetable had higher infection rate (1.25%) than people with cooked vegetable (0.74%) (P < 0.01). The population with regular massive anthelmintic drug administration had much lower intestinal parasite infection rate (0.06%) than those without implementation (1.19%) (P < 0.01). Conclusion The intestinal parasite infection rate had decreased significantly in recent years in rural area of Shandong Province and remained at low level, but whipworm infection remained high in some hilly areas and the pinworm infection kept endemic in children in plain area. People over 60 years old and preschool children are the key population who need special care for prevention and control of intestinal parasite infections in Shandong Province.