The invention relates to tubers, in particular to a tapioca starch residue separation system, which comprises a raw material cleaning machine, disintegrators, a residue-starch tank, vertical sieves, sieve cleaners, filter presses and the like. Raw materials are cleaned and crushed by a primary disintegrator and a secondary disintegrator to flow into the residue-starch tank, disintegrated residue slurry is sent by a lifting pump from the residue-starch tank to a higher primary vertical sieve, the residue slurry is separated by the primary vertical sieve, dense starch solution passes through a primary sieve cleaner to enter a raw starch tank, the separated tapioca residue is subjected to filter pressing by a primary filter press, dense starch solution and screen washing water after filter pressing pass through the primary sieve cleaner to enter the raw starch tank, fine residue passing through the primary sieve cleaner automatically flows back to the residue-starch tank, the tapioca residue after primary filter pressing enters a stirring tank to be mixed with clear water, and secondary vertical sieving, filter pressing and sieve cleaning are operated as the primary process. Reclaimed water is recyclable, the tapioca residue after secondary filter pressing is dried or directly sold, and the problems that the existing potato starch-residue separation process is complex, large in occupied space and high in operating cost are solved.