China and other developing nations face dual challenges: achieving carbon neutrality while controlling mercury (Hg) pollution across multiple environmental media (e.g., air, water, waste). To identify pathways that simultaneously reduce CO₂ and multi-media Hg emissions, we improved a typical model of human-nature system interactions. Our findings reveal that carbon neutrality efforts will play the most significant role in reducing multi-media Hg pollution. However, while end-of-pipe controls and waste recycling can lower Hg emissions in one medium (e.g., air and waste), they may inadvertently transfer pollution to another (e.g., waste and air). This study underscores the importance of whole-process management strategies to effectively tackle both climate change and Hg pollution. Simply targeting a single environmental medium is insufficient, true synergy requires integrated, cross-media solutions.