The invention discloses a human micro-ecosystem chip, and belongs to the field of medical research and human body related monitoring application. A sandwich structure of "PDMS A plate-porous membrane-PDMS B plate" is used for realizing a lower layer PDMS A plate to construct intestine-liver-heart-brain-female genital duct system to integrate an "organ chip" to simulate real human blood circulation; human microorganisms are cultured in an upper layer PDMS B plate; and a porous membrane filters human microbial metabolites from the medium containing human microorganisms, and the PDMS B plate enters the PDMS A plate. In the PDMS A plate, a micro valve is provided for micro flow between cell culture chambers, and the medium flow is adjusted by controlling the micro valve. The human micro-ecosystem chip can be used for accurately, concisely and effectively research, evaluate and control the interaction between the human microbial metabolites and multiple "organs" of an individual; and by culturing corresponding human cells in the culture chambers and controlling the flow of the culture medium, the bionics of cerebrospinal fluid circulation and direct nerve connection existing in a real human body can realized, and a research foundation is laid for medical research and human body related monitoring application.