This study investigated the biological metabolism of chlorophyll and its impact on the intestinal flora with the in vitro fermentation experiments to understand the health significance of intaking green-leafy vegetables. In the intestinal flora sequencing test of human fecal fermentation， the addition of chlorophyll reduced the diversity of flora. After 24 hours of fermentation experiments， in the chlorophyll group， the diversity index of two-years old child decreased from 2.6-3.2 to 2.4-2.7 and the diversity index of five-years old child decreased from 2.5-2.8 to 1.8-2.4. While in the field of genus， the relative abundance of Collinsella and Bifidobacterium were significantly reduced. In the change of the Bacterial metabolites， the increase of lactic acid， acetic acid was promoted by chlorophyll. Therefore， chlorophyll has a certain biological activity， which can affect the intestinal flora and its metabolites content changes.