As a commonly used additive in breeding industry, the complex pollutants and metabolites formed by antibiotics and heavy metals in aquaculture wastewater have the characteristics of strong persistence, refractory degradation and easy accumulation, and exist in the environment and human body for a long time, which caused seriously ecological, environmental and health problems. Their effective removal studies are very essential. In this paper, a CQDs-doped bifunctional molecular imprinted BiOCl/Bi3NbO7 heterojunction photocatalyst (CQDs-MIP-BNO) was fabricated and the micromorphology along with photoelectric characteristics were explored by SEM, XRD, FTIR, XPS, UV-Vis and PL analysis. The photocatalytic performance experiments implied that 10 % doping of CQDs showed the highest selectivity and photocatalytic activity for the 94 % removal rate of Ceftriaxone Sodium (CTRX) and 80 % of Cr (VI) within 45 min. On this basis, a photocatalytic reactor loaded with the as-synthesized bifunctional catalyst through a sponge mesh covered with CS/PVA film was set up and the actual operation potential was further explored. The results showed that the enhanced removal performance of this bifunctional photocatalyst for CTRX and Cr(VI) made it feasible to efficiently remove one or more low-concentration, high-toxicity antibiotics and heavy-metal pollutants from the water column to validate the utility of combining molecular imprinting and photocatalytic technologies for the treatment of aquaculture wastewater.