The perturbation of adipokinetic hormones, such as irisin, chemerin, and asprosin has been reported to participate in pathological conditions (e.g., insulin resistance) and chronic inflammation. However, exercise training has been long established as an effective intervention for prevention and treatment of these chronic and metabolic diseases. This study was to examine the effects of aerobic continuous training (ACT) and aerobic interval training (AIT) on irisin and chemerin levels of liver tissue (LT) and visceral adipose tissue (VAT), circulating asprosin, and their relationships with cardiometabolic risk factors in rats with metabolic syndrome (MetS). Thirty-two male Wistar rats were randomly divided into four equal groups: normal control (N-Ctr), control (Ctr-MetS), ACT, and AIT. After familiarization, rats with exercise intervention performed either ACT or AIT five times a week over eight weeks. The level of irisin in both ACT and AIT groups was higher than the Ctr-MetS group in LT and VAT, with a greater improvement of LT level observed in AIT vs. ACT groups. Furthermore, the level of chemerin in LT and VAT was lower in both ACT and AIT groups than the Ctr-MetS group, whereas only AIT group exhibited a reduction of serum asprosin when compared to ACT and Ctr-MetS, along with the improvements of cardiometabolic markers, such as HOMA-IR and lipid profile. These findings may support the efficiency and effectiveness of AIT intervention in the modulation of these novel metabolic hormones and cardiometabolic risk factors for reduced risk of metabolic syndrome.