Long term effects of subtotal gastrectomy on gut microbiota modifications with subsequent metabolic profiles are limited. We aimed to investigate and compare long-term effects of metabolic profiles and microbiota status in early gastric cancer patients post curative subtotal gastrectomy to the controls. In this cross-sectional study, we analyzed type II diabetes mellitus and metabolic syndrome occurrence in two groups: 111 patients after curative subtotal gastrectomy with Billroth II (BII) anastomosis and Roux-en-Y gastrojejuno (RYGJ) anastomosis and 344 age-sex matched controls. Fecal samples from those with BII, RYGJ, and controls were analyzed by next-generation sequencing method. Metabolic syndrome and type II diabetes mellitus occurrences were significantly lower in patients after subtotal gastrectomy with RYGJ than in controls over the long term (> 8 years) follow-up (P < 0.05). The richness and diversity of gut microbiota significantly increased after subtotal gastrectomy with RYGJ (P < 0.05). Compared with the control group, the principal component analysis revealed significant differences in bacterial genera abundance after subtotal gastrectomy with BII and RYGJ (P < 0.001). Genera of Oscillospira, Prevotella, Coprococcus, Veillonella, Clostridium, Desulfovibrio, Anaerosinus, Slackia, Oxalobacter, Victivallis, Butyrivibrio, Sporobacter, and Campylobacter shared more abundant roles both in the RYGJ group and BII groups. Early gastric cancer patients after subtotal gastrectomy with RYGJ had a lower occurrence of metabolic syndrome and type II diabetes mellitus than the controls during long term follow-up. In parallel with the metabolic improvements, gut microbial richness and diversity also significantly increased after subtotal gastrectomy with RYGJ.