© 2015 The Obesity Society. Objective The reports regarding the associations between childhood maltreatment (CM) and body fat composition remain heterogeneous in humans although they are indicated in preclinical studies. In addition, the effects of CM subtypes on different types of body fat are unclear. Thus, in this study, the associations between CM and its subtypes with body fat were determined and the potential pathways were explored. Methods The participants were assessed for a history of CM by the Childhood Trauma Questionnaire and were divided into the CM group (with CM exposures) and non-CM group (without CM exposures). Body composition was measured by dual-energy X-ray absorptiometry. Salivary and blood samples were provided by the subjects. Results Compared with the non-CM group, subjects with a history of CM had greater visceral fat mass (1,136 ± 160 vs. 836 ± 116 g, P < 0.05) but not total body fat, android fat, body mass index, or waist-to-hip ratio. In addition, subjects with CM had a blunted cortisol awakening response and elevated inflammatory factors. Correlation analysis indicated that CM subtypes had differential effects on visceral adiposity and cortisol awakening response. Conclusions It is suggested by our results that CM exposure is linked with increased visceral fat deposition, and the perturbation of the hypothalamic-pituitary-adrenal axis activity and activation of the immune system may be two potential pathways through which this relationship is explained.