Introduction: The aim of present study was to investigate the interaction of aerobic training and calorie restriction on levels of adiponectin isomers in serum and abdominal fat depots in obese male rats. Materials and Methods: Forty-eight wistar male rats were used as the study sample. Blood and tissue samples were collected at the 1^st, 18^th and 28^th weeks. After baseline sampling, the remaining 40 rats were randomly divided into control and high-fat-diet groups. The high-fat-diet group received their regimen for 18 weeks and were then randomly divided into the negative energy balance (NEB) and high-fat-diet (HFD) subgroups. NEB group alternately underwent 25% calorie restriction or aerobic training (running) with an intensity of 70 to 75% of vo2max for 10 weeks. Results: Compared to the standard diet, HFD feeding increased weight and decreased retroperitoneal adipose tissue adiponectin level at the 18th and 28^th weeks (P<0.05). In comparison to the HFD, group negative energy balance in obese male rats, caused weight control with significant increase in serum levels of total and high-molecular-weight adiponectin as well as adiponectin levels in retroperitoneal and mesenteric fat depots (P<0.05). Also insulin resistance index in line with serum concentrations of insulin, glucose and triglycerides were decreased in negative energy balance, compared to the high-fat-diet group (P<0.05). Conclusion: This study indicates that even with simultaneous consumption of high-fat-diet, combination of aerobic training and calorie restriction can increase concentrations of adiponectin in serum and abdominal fat depots of obese male rats, and aligned with it improves lipid and metabolic profiles.