The aim of this study was to evaluate the association between serum testosterone and abdominal body composition based on abdominopelvic computed tomography (APCT) measurements after adjusting for individual metabolic syndrome components. We performed a cross-sectional study using male subjects (age range: 22–84 years) who underwent a general health examination with abdominopelvic computed tomography and testosterone measurements. Body composition was evaluated with APCT. To confirm an association between testosterone and abdominal body composition, we conducted linear regression analysis. The effect of abdominal body composition was adjusted for important clinical factors such as age, albumin, and metabolic components in the multivariable regression analysis. Overall, 1453 subjects were included in the primary analysis. After adjustment for age, individual metabolic components, albumin, hemoglobin A1c, and C-reactive protein, we found that subcutaneous fat area index (β = − 0.042, p < 0.001), total abdominal muscle area index (β = 0.115, p < 0.001), normal attenuation muscle area index (β = 0.070, p < 0.001), and loge-transformed lower attenuation muscle area index (β = 0.140, p = 0.002) had an association with loge-transformed testosterone level. After adjusting for individual metabolic syndrome components, testosterone was associated negatively with subcutaneous fat, but not visceral fat. In addition, testosterone was positively correlated with abdominal muscle regardless of qualitative features such as fat-rich and fat-free.