Seagrass meadows are under threat due to climate change and human activities, including heavy metal contamination, which can accumulate in seagrass tissues and harm their health and productivity. Despite extensive research, effective remediation strategies are lacking. This study investigated biochar's potential as a remediation agent for seagrass meadows affected by heavy metal pollution. Heavy metal pollution was simulated by adding copper (Cu) and chromium (Cd) to seagrass Thalassia hemprichii, and the remediation effects of biochar were evaluated by monitoring seagrass physiology, root-associated microbial communities, and heavy metal concentrations. Seagrasses can accumulate heavy metals, which adversely affect their health and alter microbial communities. Seagrasses may resist heavy metal stress by releasing dissolved organic carbon (DOC) and recruiting beneficial bacteria. Biochar reduced heavy metal bioavailability and restored seagrass ecosystem health, as evidenced by restored microbial community dynamics. This study highlights biochar's promising role in seagrass meadow restoration impacted by heavy metal pollution.