Metabolic/bariatric surgery as a treatment for obesity and related diseases, such as type 2 diabetes mellitus (T2DM), has been increasingly recognised in recent years. However, compared with conventional pharmacologic therapy, the long‐term effect (≥ 5 years) of metabolic surgery in T2DM patients is still unclear. This study aimed to evaluate the diabetes remission rate, incidence of diabetic microvascular complications, incidence of macrovascular complications, and mortality in T2DM patients who received metabolic surgery versus pharmacologic therapy more than 5 years after the surgery. Searching the database, including PubMed, Embase, Web of Science, and Cochrane Library from the inception to recent (2024), for randomised clinical trials (RCTs) or cohort studies comparing T2DM patients treated with metabolic surgery versus pharmacologic therapy reporting on the outcomes of the diabetes remission rate, diabetic microvascular complications, macrovascular complications, or mortality over 5 years or more. A total of 15 articles with a total of 85,473 patients with T2DM were eligible for review and meta‐analysis in this study. There is a significant long‐term increase in diabetes remission for metabolic surgery compared with conventional medical therapy in the overall pooled estimation and RCT studies or cohort studies separately (overall: OR = 4.58, 95% CI: 1.89–11.07, P < 0.001). Significant long‐term decreases were found in the pooled results of microvascular complications incidence (HR = 0.57, 95% CI: 0.41–0.78, P < 0.001), macrovascular complications incidence (HR = 0.59, 95% CI: 0.50–0.70, P < 0.001) and mortality (HR = 0.53, 95% CI: 0.53–0.79, P = 0.0018). Metabolic surgery showed more significant long‐term effects than pharmacologic therapy on diabetes remission, macrovascular complications, microvascular complications incidence, and all‐cause mortality in patients with T2DM using currently available evidence. More high‐quality evidence is needed to validate the long‐term effects of metabolic surgery versus conventional treatment in diabetes management.