The invention discloses a gas-liquid-solid multi-phase flow reactor, and a control system and a method thereof. The reactor comprises a reactor body and a filter positioned in the reactor body, the filter comprises several filtering components with multi-loop arrangement along a circumferential part of the reactor, the control system comprises a controller, a filtering module and a backwashing module, the controller comprises a first control module, the first control module controls gradually increased filtering time of the multi-loop filtering components from an external one to an internal one, backwashing frequency is gradually reduced, and waiting time is gradually reduced. According to the invention, different filtering and back flushing operation strategies are carried out on the filters at different radial positions, the tunnel obstruction speed can be alleviated by reducing the filtering time, increasing the back flushing frequency, and increasing the waiting time on the filterwhich is nearest to the wall of the reactor, by closing to the center of the reactor by a filter core, a method of increasing the filtering time and reducing the back flushing frequency is employed, and waiting time is reduced, so that the filtering capability and the usage life of the filter core are increased.