The invention discloses an automatic-control-based denitrifying methane anaerobic oxidizing bacteria enrichment system, which comprises a methane inlet gas flow meter, an argon inlet gas flow meter, an outlet gas flow meter, a methane inlet automatic regulating valve, an argon inlet automatic regulating valve, a water inlet automatic regulating valve, an acid and alkali liquor input automatic regulating valve, a flange, a dissolved oxygen probe, a pH probe, a methane probe, a mechanical stirring blade, a reactor main body, a gas uniform distributor, a dissolved oxygen alarm, a methane alarm, a data acquisition and analysis regulating device, a biomass interceptor and a reflux pump. The invention has the advantages that: 1) the system is provided with the gas uniform distributor and the mechanical stirring blade, so that a substrate can be fully mixed with microorganisms easily, and high-efficiency enrichment is realized; 2) parameters are monitored and fed back in real time in an automatic control mode, the normal operation of the enrichment system is ensured, and manpower is reduced simultaneously; 3) the system is provided with the biomass interceptor, so that biomass is prevented from being lost; and 4) the system has a concise structure and is easy to process and convenient to universally apply.