Rural domestic sewage has the characteristics of large and scattered discharge, as well as complex components; thus, how to effectively and efficiently manage rural domestic sewage is a big challenge for policy makers. Current decentralized domestic sewage treatment facilities (DDSTF) involve different treatment processes and power drive modes; at the same time, the treatment effect is also affected by a variety of local factors. However, there is a lack of research to explore the implementation performance of the DDSTF from a comprehensive perspective. In this study, we took Nantong City, China, as a case study and conducted field investigations of 79 DDSTFs in seven counties from July 2021 to September 2022. We then made an in-depth analysis of the implementation performances of the DDSTF from an internal and external perspective. The results indicate that low temperature will reduce the DDSTF's treatment capacity, and the operation and maintenance mode affect the treatment effect of the facilities significantly. In addition, the non-standardized design for small-capacity facilities commonly results in lower compliance rates. Based on the results, we suggest that improving the quality of design and construction and adopting specialized operations are important ways to improve the treatment efficiency of rural DDSTF.