Chitosan (CTS) and capsaicin (CAP) are two kinds of effective ingredients for antiobesity, which are extracted from crab shells and Capsicum annuum. However, the strong taste of CAP makes it difficult to consume, and the antiobesity ability of CTS is limited. In this study, we prepared capsaicin-chitosan microspheres (CCMSs) by ion-cross-linking and spray drying and examined the antiobesity ability of CCMSs in obese rats. The effects of CCMSs on body weight, Lee's index, body fat, and serum lipids were investigated. The mRNA expression of PPARα, PPARγ, leptin, UCP2, GPR120, FTO, and adiponectin in the liver was determined by quantitative real-time PCR, and the protein expression of adiponectin, leptin, PPARα, UCP2, and hepatic lipase in serum was evaluated by enzyme-linked immunosorbent assay. CCMSs were prepared with 85.17% entrapment efficiency and 8.87% mean drug loading. Compared with chitosan microspheres, CAP, and Orlistat, the CCMSs showed better ability to control body weight, body mass index, organ index, body fat, proportion of fat to body weight, and serum lipids. The CCMSs upregulated the expressions of PPARα, PPARγ, UCP2, and adiponectin and downregulated the expression of leptin. CCMSs may thus be considered novel, safe, effective, and natural weight loss substances, and there is an additive effect between CTMS and capsaicin.