Background: The purpose of this research was to assess the results of eight exercise programs—Aerobic Training (AT), Resistance Training (RT), Combined Training (CBT), Electrical Muscle Stimulation Training (EMST), High-Intensity Interval Training (HIIT), Whole Body Vibration Training (WBVT), Stretching Training (STT), and Other Training (OT)—on anthropometric measurements and intermediate disease biomarkers in obese individuals aged 18 and above. Methods: A systematic review was undertaken, searching databases such as CNKI, Web of Science, PubMed, Embase, Cochrane Library. Only Randomized Controlled Trials (RCTs) focusing on the influence of these eight exercise interventions on anthropometric outcomes and intermediate disease markers in obese patients were included. The methodological quality of the chosen studies was evaluated using the Cochrane Risk of Bias Assessment Tool. Specialized data analysis software was then used for subsequent analyses. Results: Clinical trials conducted from May 2009 to August 2023 were considered. A total of 119 studies were incorporated, with an aggregate sample size of 5,537 participants. Network meta-analysis showed that Resistance Training significantly improved LDL cholesterol levels (SUCRA: 60.4%); Combined Training prominently enhanced HDL cholesterol levels (SUCRA: 78.5%); and HIIT led to a substantial decrease in TC levels (SUCRA: 78.2%). Conclusions: Based on network ranking diagrams, combined training—merging aerobic and resistance exercises—seems optimal for obese patients. This modality demonstrates notable efficacy in reducing body weight and fat percentage, and concurrently improves HDL cholesterol, blood glucose levels, maximal oxygen uptake, and IL-6 levels.