Background: Stomach adenocarcinoma (STAD) ranks as the second incidence rate in China. The MisMatch Repair (MMR), composed of MLH1, MSH2, MSH3, MSH6, and PMS2, is a critical mechanism for repairing DNA error. In case of microsatellite instability (MSI), the MMR system is capable of repairing the mismatches. MSI-high (MSI-H) is created as a result of deficient mismatch repair (dMMR). A numerous studies have established the clinical importance of both MSI and MMR for the diagnosis, prognosis, and treatment of STAD. Circulating tumor DNA (ctDNA) provides a non-invasive method for the diagnosis and prognosis of cancer. The examination of MMR-related gene mutations in STAD can serve as a means of evaluating the utility of ctDNA in detecting. Methods: MMR-related genes list was collected from relevant literature. The clinical and genetic mutation data of 441 STAD samples were obtained from cBioPortal. Kaplan-Meier survival analysis was used to evaluate the total survival rate (OS) of the published STAD data set. 680 STAD patients with TP53 mutation were screened and analyzed from the HapLab database. Results: An analysis of the TCGA data indicated that 356 patients had wild-type MMR genes and 85 had MMR mutations. MSH3 mutations accounted for 19.27% of the overall mutations and 42.35% of patients with MMR mutations, with a total of 36 patients. In terms of OS, patients with MMR gene mutations had a better prognosis compared to those with wild-type genes (log-rank test, p-value = 0.028). In the single-gene prognostic analysis, patients with MSH3 mutations had better prognosis (p-value 0.0004), while no statistical differences were found in other genes. In the monitoring of 680 HapLab STAD patients using ctDNA, 12.35% (84/680) had MMR mutations in their tumor tissue. After treatment, the proportion of TP53 mutations detected in patients was 11.91% (81/680), while the proportion of MMR mutations was 3.57% (3/84). Conclusions: The results of survival analysis showed a significant association between the mutation status of MMR and STAD. Monogenic MSH3 mutations was highly associated with the better survival, and circulating tumor DNA in blood highlight the importance of detecting MMR mutations in STAD patients. ctDNA provides a non-invasive method for the assessment of prognosis in STAD patients through the analysis of MMR gene mutations.