Background: Synchronous multiple primary colorectal cancer (sMPCC) is clinically rare while its incidence was increasing in the past decade. However, little was known about molecular and clinical features of sMPCC, which might be different from single primary colorectal cancer (CRC). Methods: From November 2012 to April 2021, 239 sMPCC from a total of 13276 CRC patients operated in the 6^th Affiliated Hospital of Sun Yat-sen University were enrolled in this study. Mismatch repair (MMR) status in each lesion of all 239 patients was examined by immunohistochemistry (IHC). Totally 78 sMPCC patients and 94 single primary CRC patients conducted an 831-gene panel based next-generation sequencing (NGS) (OncoPanscan, Genetronhealth). Somatic mutations and potential pathogenic germline variants were analyzed. Microsatellite instability (MSI) and tumor mutation burden (TMB) were calculated. Results: We found that dMMR/MSI-H frequencies in sMPCC were significantly higher than those in single primary CRC, which were confirmed by both IHC (50/239 vs 872/13037, p< 0.001) and NGS (17/78 vs 5/94, p = 0.0022). According to the MMR/MSI status at different lesion in sMPCC patients, they were further divided into all MSI-H, MSI-H & MSS and all MSS group, with incidences of 16.7%, 4.2% and 79.1%, respectively. With NGS analysis, we found that the most enriched gene mutation type in sMPCC patients was C > T (G > A), and their most frequently mutated genes were APC (65%), KRAS (46%), TP53 (31%), PIK3CA (25%), EGFR (23%), ARID1A (18%), NF1 (18%), SOX9 (18%), FAT4 (16%), and TCF7L2 (15%), whereas those genes in single primary CRC patients were APC (71%), TP53 (64%), KRAS (40%), FBXW7 (20%), PIK3CA (13%), SMAD4 (12%), ARID1A (11%), FAT4 (11%), CREBBP (11%), and NF1 (10%). Moreover, we found that higher TMB was correlated with higher MSI in sMPCC rather than single primary CRC patients. Furthermore, we found that the mutated genes were different among three subgroups. The top 5 mutated genes in MSI-H group were APC (68%), FAT4 (64%), TCF7L2 (59%), KMT2B (55%), ARID1A (45%), whereas those in MSI-H & MSS group were APC (57%), KMT2B (43%), KMT2C (43%), ATM (43%), PRKDC (43%), and those in MSS group were APC (66%), KRAS (49%), TP53 (36%), PIK3CA (21%), EGFR (20%). Finally, we also found that patients with pathogenic/likely pathogenic germline mutations were comparable between sMPCC and single primary CRC, indicating that sMPCC may not be resulted from germline changes. Conclusions: Our results revealed that incidences of dMMR/MSI-H in sMPCC were significantly higher than those in single primary CRC. We proposed that MMR/MSI status of each lesion in sMPCC patients should be verified before treatment and these patients could be divided into three subgroups according to their MMR/MSI status. Our findings indicated that sMPCC patients with different MMR/MSI status might be treated with personalized therapies for better management of their disease.