Crude Cordyceps militaris polysaccharides (CMPs) have been proven to be effective in alleviating harmful effects of a long-term high-fat diet (HFD), but there are fewer related studies on identifying the health-regulating abilities of certain subcomponents of CMPs. This study aimed to figure out the main component of CMPs in anti-obesity and to further explore its regulatory effects in vivo. Results showed among three main subcomponents (CMP40, CMP60 and CMP80) of CMPs, the large molecular weight CMP40 (with average molecular weight of more than 100 kDa) has shown superior in vitro hypoglycemic and hypolipidemic capacities. The simultaneous intervention of CMP40 indicated that it could reduce the body weight and white adipose tissue mass/area in the HFD mice. Serum parameters also suggested a decrease in the cholesterol and triglyceride level in the CMP40 group. These results might be due to the down-regulation of lipid synthesis and the up-regulation of lipolysis pathways. Besides, CMP40 could alleviate the inflammatory condition, such as the lower LPS and inflammatory cytokines levels, in the HFD mice in a dose-dependent manner. It could also restore gut health by increasing the SCFAs level, regulating gut microbiota structure, and repairing intestinal tight junction. Results also confirmed safe in CMP40 consumption since there were no side-effects on a high concentration addition of CMP40 (8%) to a regular diet. These findings suggested the promising anti-obesity effect of CMP40 and provided a theoretical basis of its further application in food industry.