The invention provides a microwave multi-effect filtering system, and belongs to the technical field of industrial wastewater treatment. The microwave multi-effect filtering system comprises a separation box, a putting-in opening, a mixing box, a connecting pipe and separation boxes, the putting-in opening is formed in the top of the separation box, the mixing box is arranged at the bottom of the separation box, the separation box communicates with the interior of the mixing box, and a plurality of separation boxes are arranged on one side of the mixing box. The mixing box communicates with the separation boxes through a plurality of connecting pipes, a notch is formed in one side of each separation box, an isolating mechanism for primarily filtering wastewater is arranged at the position, located at the notch, in each separation box, and a locking mechanism for locking each isolating mechanism is arranged in the corresponding separation box. Under the action of the isolating mechanisms, large sundries such as gravels, wood blocks and plastics contained in waste water are removed, and the primary filtering effect is achieved. Under the action of the locking mechanisms, installation of the isolating mechanisms is achieved. Under the action of a damping assembly, the impact force generated when the waste water is thrown into the separation boxes is reduced, and the situation that the isolation mechanismes are impacted by the wastewater for a long time and damaged is avoided.