Heavy metals (HM) are ubiquitous in environments, and HM pollution has become a severe global crisis. Previous studies have identified HM levels in Qinling panda habitats but their levels and the associated risks in Sichuan panda habitats are still unknown. Risk-based conservation management is in urgent need and should rely upon identifying risk distributions, quantified risk-source apportionment and collaborative governance. We carried out research in Sichuan panda (Ailuropoda melanoleuca melanoleuca) habitats taking soil, bamboo, and water samples from three different areas (nature reserves, potential habitats, and surrounding regions) of five mountains. The concentrations of HM in the soil were higher than those in bamboo, but both exceeded the background or national standards to varying degrees, suggesting long-term pollution and multi-element contamination. Regional and geographical distribution differences revealed a positive correlation between intensity of human activities and HM pollution. HM contaminants observed in the Sichuan panda habitats, based on their sources, were categorized into coal combustion (34%), industry (44%), and traffic (22%). In particular, our results showed the northern and southern parts of habitat were of highest concern, as they had environmental conditions that could be harmful to the health of giant pandas. Coupling models applying positive matrix factorization model/risk were used to quantify source contributions to various risk types, which was based on real-time monitoring and served as a positive role in multi-step process for developing countermeasures, with the goal of collaboratively reframing the vision and governance of panda conservation in order to incorporate regional disparities.