The aim of this study is to investigate the impact of exercise on intermediate disease markers in populations with overweight and obesity, providing evidence-based recommendations for clinicians to utilize these markers in developing exercise prescriptions for this group. The study was conducted by retrieving data from PubMed, Embase, Cochrane Library, Web of Science, and CNKI and only including Randomized Controlled Trials (RCTs) to examine the effect of different exercise interventions on intermediate disease markers in overweight and obese people. The quality of the included studies was evaluated using the Cochrane Bias Risk Assessment tool and the data was analyzed using Stata 15.1 data analysis software. The RCTs were collected from January 2017 to March 2024. A total of 56 RCTs were included and the results of 10 outcomes were analyzed using random effects meta-analysis. The total sample size used in the study was 3193 The results showed that resistance training significantly reduced total cholesterol (SUCRA: 99.9%), triglycerides (SUCRA: 100.0%), low-density lipoprotein (SUCRA: 100.0%), systolic pressure (SUCRA: 92.5%), and increased high-density lipoprotein (SUCRA: 100.0%). Aerobic exercise significantly reduced insulin (SUCRA: 89.1%) and HbA1c (SUCRA: 95.3%). Concurrent training significantly reduced HOMA-IR (SUCRA: 93.8%), diastolic blood pressure (SUCRA: 71.2%) and Glucose (SUCRA: 87.6%). Exercise has a significant impact on intermediate disease markers in populations with overweight and obese. Compared with no exercise, exercise lowers total cholesterol, triglycerides, LDL, systolic blood pressure, diastolic blood pressure, HOMA-IR, insulin, and HbA1c, and increases HDL in people with overweight and obese. These findings provide evidence-based recommendations for exercise interventions aimed at weight reduction and the prevention of chronic diseases in individuals with overweight and obese.