Chitosan and capsaicin are compounds extracted from natural products and have been indicated to lower body weight and prevent fatty liver. However, their applications are limited by poor oral bioavailability, low compliance and some serious side effects. To solve these problems, we successfully prepared chitosan microspheres (CTMS) and chitosan-capsaicin microspheres (CCMS) in previous study. Therefore, in the present study, we evaluated the ability of CTMS and CCMS to eliminate lipid accumulation in hepatocytesand also characterized their pharmacokinetic parameters after administration. The results showed that the two microspheres could significantly reduce intracellular lipid accumulation and dose-dependently improve the triglyceride (TG) content in HepG2 cells. A pharmacokinetic study indicated that CTMS and CCMS were distributed in almost all of the measured tissues, especially liver and kidney, and that their absorption was better than those of chitosan and capsaicin. Simultaneously, the prolonged circulating half-lives, the lower clearance and higher plasma concentration of CTMS and CCMS showed that their bioavailability was effectively enhanced. All of the results indicated that the lipid accumulation inhibition of CTMS and CCMS was better than that of chitosan and capsaicin, and that these microspheres can be developed as preventive agents for fatty liver or obesity.