In this research， the metabolism sites of chlorophyll and its derivatives in rats were studied by 24 hour metabolism experiment. Under acid conditions， in stomach， Chlorophyll a would be immediately degraded into pheophytin a， accompanying with production of a little amount of chlorophylide， while Chlorophyll b was relatively stable. Chlorophyll was rarely absorbed in the rats’ stomachs； the amount of entry in large intestine were relatively around 84%， and the excrement rate in the feces was about 43%， whereas nothing was detected in the blood and urine. The results of analysis of gut microbiota and their metabolites showed that the ingestion of chlorophyll changed the composition and abundance in the sequencing of the fecal microbiota. The relative abundance of Proteobacteria was significantly reduced， while Akkermansia and Lactobaillus were significantly increased. And chlorophyll promoted the increase of acetic acid， propionic acid and citric acid.