The invention relates to an automatic anaerobic three-phase separation system and a control method. The system comprises a reactor, a three-phase separator arranged inside the reactor, and a water-sealing assembly and a controller which are arranged outside the reactor, wherein the three-phase separator comprises a plurality of gas collecting hoods arranged in parallel, a gas collecting pipe communicating with the upper ends of the gas collecting hoods, and a gas chamber liquid level gauge installed on the upper end of any one gas collecting hood, the water-sealing assembly comprises a water-sealing tank, and a gas outlet pipe, a water inlet pipe, a water outlet pipe and a water-sealing liquid level gauge which are installed on the water-sealing tank, the gas collecting pipe extends into the water-sealing tank, a first valve is installed on the water inlet pipe, a second valve is installed on the water outlet pipe, and the controller is electrically connected with the gas chamber liquid level gauge, the water-sealing liquid level gauge, the first valve and the second valve, respectively. The three-phase separation system consisting of the three-phase separator with a double-layer inverted V-shaped structure, and a water-sealing tank is adopted, and the gas chamber pressure can be automatically adjusted through the coordinated control of the controller to match system operation.