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The application discloses a high-concentration hydrogen-methane co-production microbial electrochemical system, which comprises an inlet and outlet module, a microbial electrolysis module and a gas collection module, the microbial electrolysis module comprises an electrochemical workstation and a reaction chamber, the reaction chamber comprises an anode chamber and a cathode chamber, the bottom of the anode chamber and the cathode chamber is respectively provided with an anode chamber connecting port and a cathode chamber connecting port, the anode chamber connecting port and the cathode chamber connecting port are connected, a proton exchange membrane is arranged in the middle, the top of the anode chamber is respectively provided with an anode chamber inlet port, an anode chamber electrode port and an anode chamber gas outlet port, the top of the cathode chamber is respectively provided with a cathode chamber inlet port, a cathode chamber electrode port and a cathode chamber gas outlet port, the inside of the anode chamber and the cathode chamber is respectively provided with a carbon brush anode and a carbon cloth cathode, the carbon brush anode and the carbon cloth cathode are led out through the anode chamber electrode port and the cathode chamber electrode port respectively and are connected with the electrochemical workstation, organic wastewater is treated, and methane with a concentration of more than 95% and hydrogen with a concentration of 30%-90% are independently generated and collected.