In the context of sustainable development, a number of rural domestic sewage treatment facilities had been built in China to solve the problem of rural domestic sewage pollution. The comprehensive, quantitative and objective efficiency assessment of facilities is urgent. This study used a non-radial slacked-based data envelopment analysis model combined with cluster analysis to construct an index system covering multiple aspects, including three inputs and four outputs to assess 681 facilities. These samples selected from the biggest demonstration area are the most representative for and exceed 2/5 of the running facilities all over the country. The average efficiency score of samples was 0.496 meaning the improvement potential was about 50.4%. Only 27 samples were relatively effective, scoring 1. The remaining 654 facilities had different levels of input excesses or output shortfalls, which should be the key objects to improve overall performance. In addition, there was evidence that output indicators had more room for improvement than input indicators. The analysis of sensitivity on inputs and outputs confirmed that the idleness and poor treatment effects of rural sewage treatment facilities should be concerned. Finally, Kruskal–Wallis non-parametric test verified that technology and load rate of facilities have significant impacts on efficiency. The performance evaluation results could not only provide guidance for the local government to strengthen the supervision and operation of facilities, but also potentially provide reference for the construction, operation and management of rural sewage treatment facilities in China