The utility model relates to the technical field of biological medium separation, and discloses anti-clogging biological medium separation equipment, which comprises a cleaning mechanism, a shell and a clamping mechanism, the cleaning mechanism comprises two pull rods, a filter frame and a turntable, the bottoms of the two pull rods are fixedly connected with scrapers, the bottom of the filter frame is movably embedded in the inner wall of the top of the turntable, and the clamping mechanism is fixedly connected with the shell. The outer wall, close to the bottom, of the filter frame is fixedly connected with a bottom ring, the inner wall, away from the center, of the bottom ring is rotatably connected with a plurality of first bolts, the clamping mechanism comprises a plurality of clamping frames, the inner walls of the clamping frames are slidably connected with clamping plates, and the positions, close to the two sides, of the clamping plates are each in threaded connection with two second bolts; filter membrane paper is movably connected between the clamping plates and the clamping frames and located on the faces, close to the centers, of the filter frames. According to the utility model, the subsequent medium separation quality can be ensured through the arrangement of the cleaning mechanism, and the medium separation quality can be ensured through the arrangement of the clamping mechanism.