Perinereis aibuhitensis (Grube, 1878) lives in marine sediments of estuary or shoal areas, where substrate has some crucial environmental factors affecting its burrowing and distribution. In order to provide basic data for the habitat selection and suitability evaluations of the artificial aquaculture of P. aibuhitensis, this paper conducted a quantified analysis of its burrowing ability and explored its behavioral preferences in different substrates, including mud (<75 μm), fine sand (125–250 μm), medium sand (250–500 μm), coarse sand (500–2 000 μm), gravel (2 000–4 000 μm) and ceramsite (4 000–8 000 μm). The research results revealed that substrate grain size significantly affected the burrowing time, burrowing rate, burrowing depth and distribution rate (P<0.01). Moreover, P. aibuhitensis demonstrated preferential selections relating to substrate grain sizes, had higher burrowing ability in ceramsite, mud and fine sand compared with other substrates. The strongest burrowing ability and the highest distribution rate were observed in ceramsite. The study indicated that P. aibuhitensis was sensitive to substrate grain size, which also had an impact on its burrowing process and population distribution. In the natural sea, substrates mainly composed of mud and fine sand are fit for aquaculture and stock enhancement. Based on behavioral preferences and ecological rehabilitation function of P. aibuhitensis, this paper proposes a symbiotic system of marine animals and halophytes, and constructs an ecosystem model of " Marine fish-Halophytes-Perinereis aibuhitensis” with P. aibuhitensis as the link.