Background Identifying genetic disease-susceptible individuals through population screening is considered as an effective approach for disease prevention. DNA mismatch repair (MMR) genes including MLH1, MSH2, MSH6 and PMS2 play essential roles in maintaining microsatellite stability through DNA mismatch repair, pathogenic variation in MMR causes microsatellite instability and is genetic predisposition for cancer as represented by the Lynch syndrome. While the prevalence and spectrum of MMR has been extensively study in cancer, it remains largely unclear in the general population. Lack of the knowledge prevent it from effective prevention MMR variation related cancer. We addressed the issue using the Chinese population as a model. Methods We performed extensive data mining to collect MMR variants derived from 18,844 Chinese individuals, and comprehensive analysis of the MMR variants to determine its prevalence, spectrum, and multiple features of the MMR data. Results We identified 17,687 MMR variants. We observed substantial differences of MMR variation between the general Chinese population and Chinese cancer patients, identified highly Chinese-specific MMR variation through comparing MMR data between Chinese and non-Chinese populations, predicted the enriched deleterious variants in Chinese-specific MMR variants, determined the MMR pathogenic prevalence of 0.17% in the Chinese population, and determined that MMR variation in general Chinese population is evolutionarily neutral. Conclusion Our study provides a comprehensive view for MMR variation in the general Chinese population , a reference for planning population screening for MMR-related cancer prevention, and a resource for biological study and clinical applications of human MMR variation.