[Objectives] To provide a theoretical basis for constructing the best species suitable for local shrimp-bivalves-algae IMTA through the screening of different bivalves and the determination of seaweed density. [Methods] The preliminary studies of different kind of bivalves and macroalgae (Gracilaria lichevoides) used for the purification of shrimp effluent were described. Through the screening of benthic bivalves, the best ratio of integrated culture of bivalves and algae was determined. [Results] Both bivalves and macroalgae had certain purification effects on aquaculture wastewater, but the effects significantly differed from species and breeding density. The removal rate of nutrient declined from Potamocorbula laevis, Sinonovacula constricta, Tegillarca granosa. The mixotrophic culture of 8 ind/L P. laevis and 120 g G. lichevoides had the highest efficiency of purification and removal rates of nutrient: NH4-N: 90.67%, TP: 86.18%, TN: 72.66%, NO3-N: 51.85%, respectively. There was a significant difference between the blank control group and the other three groups (P<0.01). The 8 ind/L + 120 g group was significantly higher than the 4 ind/L + 120 g group (P<0.05) in TP removal rate. Additionally, the difference between four groups was significant in the removal rate of NH4-N and TN (P<0.05), but 2 ind/L + 120 g group and 8 ind/L + 120 g group in the removal rate of NO3-N had no significant difference (P>0.05). [Conclusions] This research provides a reference for the use of filterable shellfish and large seaweed to treat aquaculture wastewater, and also provides the theoretical basis for constructing the local multi-level breeding structure.