The invention discloses a method for solving the problem of biological deposition of a sand-bottom stichopus japonicus aquaculture pond by the aid of biological functions. The method can solve problems that an effect for improving biological deposition of a sand-bottom stichopus japonicus aquaculture pond is poor in the prior art, a sedimentary environment of the stichopus japonicus aquaculture pond cannot be effectively improved, diseases of stichopus japonicus cannot be prevented and the like. The method is characterized in that certain quantities of penaeus japonicus, fenneropenaeus chinensiss, ruditapes philippinarum and sinonovacula constricta are fed into the stichopus japonicus aquaculture pond, an effect of loosening the bottom of the pond is realized owing to sand diving functions of the penaeus japonicus, the fenneropenaeus chinensiss, the ruditapes philippinarum and the sinonovacula constricta, organisms such as nereid and copepoda in the aquaculture pond are ingested by the penaeus japonicus and the fenneropenaeus chinensiss, and residual feeds, organic detritus, humus, fungi and the like are subjected to filter-feeding by the ruditapes philippinarum and the sinonovacula constricta. Accordingly, the method has the advantages that the purpose of improving a sedimentary environment of the aquaculture pond is achieved, and the problem of biological deposition of the aquaculture pond is solved.