Objective To investigate the metabolic mechanism of the extract of Coix seed to regulate free fatty acid（fats） of NAFLD（non-alcoholic fatty liver disease） in rats. Methods 30 adult rats were selected to make NAFLD models. They were randomly divided into model group， high-dose group and low dose group with 10 rats in each group. Meanwhile， 10 healthy rats were selected as control group， and the metabolic indexes of four groups were compared. Results Compared with control group rats， the rats in the model group TC， FFA increased and ADP decreased（P<0.05）， the rats in the treatment group TC， FFA and ADP was significantly lower than that of model group was higher than in the model group（P<0.05）， different doses of rats to form comparison have significant difference（P<0.05）； compared with normal rats， the rats in the model group significantly increased ALT and AST（P<0.05）， the treatment of ALT and AST levels in rats was significantly lower than that of model group（P<0.05）， the high dose group rats were significantly lower than that of low dose group rats（P<0.05）； AMPK activity model rats were lower and FAS， ACCa-se expression increased significantly（P<0.05）， the treatment group rats increased AMPK activity and FAS， ACCa-se expression decreased significantly（P<0.05）， different doses of rats to form comparison have significant difference（P<0.05）. Conclusion The extract of Coix seed can effectively improve the level of adiponectin in NAFLD rats and induce the lipid metabolic reaction in the lower reaches， thus improving the metabolism of free fatty acids.