Abstract: Cage aquaculture plays an essential role in marine aquaculture. However, the negative impact of biofouling shortens the cleaning cycle of the cage, leading to increased maintenance cost. Additionally, biofouling obstructs oxygen supply and waste removal from the cage, heightening the risk of infection among aquatic organisms. This issue poses a significant challenge to the advancement of aquaculture. Currently, methods to combat marine biofouling mostly remain in the laboratory stage because of the tedious production process and lack of practical verification. Therefore, it is meaningful to develop an economical and effective antifouling coating for aquaculture cages. Biofilm formed by bacteria and diatoms facilitate the settlement of marine invertebrates such as Mytilus coruscus, which is the key to solve the problem of marine biofouling. Polydimethylsiloxane (PDMS) is a typical fouling-release coating known for its viscoelasticity and hydrophobicity. The lack of mechanical strength and the performance of long-term confrontation with diatom adhesion uncovered the limitations of PDMS. The conventional solution is to incorporate other materials into PDMS, which can improve the mechanical properties of PDMS and allow PDMS to inhibit the microfouling formed by bacteria and diatoms. Nano-zinc oxide particles (ZnO NPs) are characterized by small particle size and high specific surface area, showing excellent antibacterial properties, which can be combined with PDMS as a bacteriostat. In this study, ZnO/PDMS coating made from PDMS filled with different concentrations of ZnO NPs was used to improve the antifouling ability of cages. The effects of Glass, PDMS, and ZnO/PDMS (ZnO NPs concentrations of 3.5wt%, 7.5wt%, 11.25wt%, and 15wt%) on natural biofilms and subsequent mussel settlement were tested in field bioassay. Compared with Glass and PDMS, the settlement rate of M. coruscus decreased by 75.41% and 62.50%, respectively, on 15wt% ZnO/PDMS-coated surfaces with 28-day-old biofilms. Furthermore, at 28 days of age, the bacterial density of the biofilm formed on 15wt% ZnO/PDMS was reduced by 43.25% and 40.44%, respectively, compared to Glass and PDMS. The diatom density decreased by 91.59% and 13.32%, respectively, compared with Glass and PDMS in 28-day-old biofilm. MiSeq sequencing confirmed differences in bacterial communities among substrates. Representatively, the relative abundance of Psychrobacter decreased, while the relative abundance of Winogradskyella increased on 15wt% ZnO/PDMS. Structural Equation Model results indicate that ZnO/PDMS could inhibit M. coruscus attachment by reducing natural biofilm biomass and changing the bacterial community. This study fills the gap in the effect of ZnO/PDMS coating on the bacterial community of natural biofilms and provides a novel solution for the biofouling in cage aquaculture.