Objective To evaluate the effectivenss of innocent sanitary toilets improvement in rural areas of Jiangsu Province during 2016—2020. Methods Two villages from one county (city, district), which was randomly selected from each of the 13 cities in Jiangsu Province were set as investigating sites. Ten or more households with toilets renovated from 2016 to 2020 were randomly selected from each village for the household site-visit to collect the information of general condition of household toilet reconstruction, the type of septic tank and its effective volume, and the outflow of the fecal fluid of the third compartment. Fecal fluid samples from the first and third compartment were collected to examine the fecal coliform value, five-day biochemical oxygen demand (BOD5), chemical oxygen demand (COD), ammonia nitrogen (AN) and parasite eggs. Household questionnaire was conducted to collect the information of residents’ satisfaction with toilet improvement and the way using fecal manure. The overall incidence of intestinal infectious diseases during 2016—2020 was retrieved from the data reported by local township health clinics. Furthermore, the economic expenditures caused by intestinal infectious diseases were also collected in the year of 2015 and 2020 in each investigated village. Paired t test was used for the difference comparison of fecal coliform value, COD, BOD5 and AN between the first and third tank compartments. Results Totally 367 households from 26 administrative villages were investigated. The main type of septic tank were constructed with brick and prefabricated cement parts, each type of which accounted for 42.7% (157/367) and 24.5% (90/367), respectively. The septic tanks with effective volume reaching 1.5 m³ accounted for 93.0% (279/300). The fecal fluid from the tank-third compartment was mostly used as field fertilizer (212/290). The coliform values of fecal fluid in first and third compartment were (119.8 ± 33.4) and (42.0 ± 18.5) coliform/ml, with significant difference between the compartments (t = 6.534, P < 0.01). The concentrations of BOD5, COD and AN in the fecal fluid in the tank-first compartment were (354.7 ± 124.8), (1 021.8 ± 352.5) and (119.2 ± 64.3) mg/L, while those in the tank-third compartment were (138.6 ± 62.4), (531.1 ± 229.6) and (96.3 ± 42.7) mg/L, repectively, with significant differences between the first and the third tank compartment (t = 5.042, 9.631, 2.455, P < 0.01). No human parasite eggs were detected from all fecal fluid samples. From 2016 to 2020, the incidence of overall intestinal infectious diseases in the community (towns) that the surveyed village affiliated to was reduced from 24.6/100 000 in 2016 to 4.3/100 000 in 2020. A total of 305 household questionnaires were performed and the awareness rate of toilet related knowledge, the positive support to toilet renovation and the satisfaction rate in this aspect reached to 95.1% (290/305), 100% (303/303), and 96.7% (291/301), respectively. The publicity materials were accessible in 88.5% (270/305) residents’s home, and 96.1% (293/305) residents knew that the fecal fluid in tank-third compartment were used as fertilizer. In 2020, the intestinal infectious diseases cost the surveyed village 81 000 Yuan, which decreased by 53.9% compared with 176 000 yuan in 2015. Conclusion During 2016 to 2020, the accomplishment of household toilet harmless-renovation reached to the defined standard of feces harmless sanitary management in rural areas of Jiangsu Province, which could be conducive to control the transmission of infectious diseases via night soil-mouth route, including intestinal parasitic diseases, as well as to improve sanitary conditions and protect people’s health.