This study examines the effects of aerobic, resistance, and combined exercise on metabolic syndrome parameters and cardiovascular risk factors, to identify the most effective way of improving metabolic syndrome and preventing cardiovascular disease. We searched EM BASE, the Cochrane Library, PubMed, MEDLINE, Ovid, the Chinese Biological Medicine Database (CBM), the Wanfang Database, the China National Knowledge Infrastructure (CNKI) database, and the Chinese Scientific Journal Database (VIP), for randomized controlled trials (RCTs), identifying 15 comparing the effects of aerobic, resistance, and combined exercise on metabolic syndrome parameters and cardiovascular risk factors (e.g., glucose, triglyceride, blood pressure, body mass index, etc.). We assessed the quality of the articles and performed a network meta-analysis with a Bayesian random effects model to synthesize direct and indirect evidence. Combined exercise was most effective at controlling glucose and total triglyceride (TG) levels. Aerobic, resistance, and combined exercise groups achieved significant effects regarding body fat. Aerobic exercise was superior to resistance exercise regarding body mass index (BMI). There was no statistically significant difference in weight, waist circumference (WC), levels of high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), insulin, systolic blood pressure (SBP), and diastolic blood pressure (DBP) among the exercise groups. Combined exercise was the best exercise scheme for improving weight, WC, DBP, TG, TC, glucose, and insulin levels. Resistance exercise was most effective at ameliorating body fat, LDL-C levels, and SBP. Aerobic exercise was the optimal way of improving BMI and HDL-C levels. This network meta-analysis suggests combined exercise is the most effective choice in improving the metabolic syndrome and cardiovascular risk parameters, whereas aerobic exercise reveals the minimum effect. Further studies should certify the role resistance exercises play in metabolic syndrome and cardiac rehabilitation.