China and many developing countries face dual challenges in achieving carbon neutrality and controlling multi-media Hg pollution. Previous studies have employed computable general equilibrium models to assess China’s atmospheric Hg emissions under various CO2 mitigation and end-of-pipe Hg control scenarios. However, these models rely on highly aggregated sectoral classifications, failing to differentiate between specific technologies with varying Hg emission factors. Moreover, these studies overlook Hg emissions to other environmental media, particularly industrial waste, which can later re-emit Hg into the atmosphere during waste recycling processes. Given that comprehensive utilization of industrial waste is widely recognized as an effective CO2 reduction strategy, identifying pathways that synergistically mitigate both CO2 and multi-media Hg emissions is crucial. To address these gaps, we selected and enhanced the technology-rich integrated assessment model GCAM-China. First, we disaggregated non-ferrous metal smelting sectors (including zinc and lead smelting) from other industry, as these are major sources of both CO2 and multi-media Hg emissions. Next, we incorporated cement production technologies that co-process industrial waste, given the cement sector’s role as a primary sink for such waste. Finally, we integrated multi-media Hg emission factors and industrial waste generation rates into key GCAM-China sectors, enabling the model to simultaneously estimate CO2 emissions, multi-media Hg emissions, and industrial waste generation. Using this improved framework, we developed scenarios aligned with China’s carbon neutrality goals, end-of-pipe Hg controls, and industrial waste utilization. Preliminary results indicate that achieving carbon neutrality will be the primary driver of multi-media Hg mitigation, reducing atmospheric Hg emissions by 52.9%, aquatic Hg releases by 87.1%, and Hg entering industrial waste by 79.8%. However, while end-of-pipe controls and waste utilization can reduce Hg emissions in one environmental medium, they may inadvertently shift pollution across media. These findings highlight the need for whole-process control strategies to effectively address both climate change and multi-media Hg pollution.