Mariculture sediments have been exchange and propagation sources of antibiotic resistance genes (ARGs). However, no efficient methods have been generated to remove ARGs from sediments. Here, we explored the impact of hydrogen peroxide (H2O2) and aeration on the efficient removal of ARGs and mobile genetic elements (MGEs) in mariculture sediments. When compared with the aeration group, the ARG abundance was 3.8-32.3% lower in the H2O2 group during the first 14 days. ARG and MGE abundances were also significantly associated with reduced total bacterial population and diversity (P < 0.05). Based on partial squares path modeling, reduction of MGEs had important roles in ARG removal from H2O2 treatments, while in the aeration group, ARG reductions were mainly determined by changes in bacterial community composition. These results suggested that H2O2 treatment represent a promising method for controlling ARG abundance after dosing feed stuff and limit the spread of ARGs in aquaculture environments.