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Objective To compare the effects of two exercise intensities on metabolic syndrome (MS). Methods Forty-nine MS patients hospitalized in Taiyuan Central Hospital from December, 2022 to January 2024 were selected and randomly divided into two groups : a standard group (n = 24) and individual group (n = 25). All patients underwent cardiopulmonary exercise test ( CPET) before and after treatment, collecting major indexes including body parameter, body component, and metabolic indicator for prescribing exercise programs. The standard group was trained with exercise intensity prescribed on heart rate reserve, while the individual group received the exercise with intensity prescribed on ventilatory threshold. Both groups received equal energy consumption exercise intervention with the same exercise frequency for 12 weeks. Results The two groups demonstrated significant improvements in waist circumference (WC), body mass index (BMI), body fat related indexes, and systolic blood pressure after intervention (P < 0.05). The individual group showed significant improvements inWC, BMI and body fat related indexes as compared to the standard group (P < 0.05). Both groups showed significant improvements in peak oxygen uptake, (PeakVO2), peak load power (Peak WR), peak metabolic equivalent (PeakMets), and peak respiratory exchange ratio ( Peak RER ) after intervention (P < 0.05 ). The individual group presented significant improvements in peak heart rate (HRpeak), peak oxygen pulse (Peak VO2/HR), and maximum voluntary ventilation (MVV) (P < 0.05) after intervention. Before intervention, the standard group demonstrated significantly higher levels in PeakVO2 and Peak MET compared to the individual group (P < 0.05), but after intervention the two groups showed no significant differences in the two indexes. After the intervention, the individual group demonstrated insignificant improvements in all indexes compared to the standard group (P > 0.05). Conclusions Both exercise prescriptions based on CPET can effectively improve the health-related indicators of MS patients on condition of moderate exercise intensity. However, the program prescribed based on individualized ventilatory threshold shows superiority to the program prescribed based on maximum physiological value in improving these indicators. [ABSTRACT FROM AUTHOR]