Heavy metals can severely influence the mineralisation of organic pollutants in a compound-polluted environment. However, to date, no study has focused on the effects of heavy metals on the active organic pollutant-degrading microbial communities to understand the bioremediation mechanism. In this study, toluene was used as the model organic pollutant to explore the effects of soils with different levels of heavy metal pollution on organic contaminant degradation in the same area via stable isotope probing (SIP) and 16 S rRNA high-throughput sequencing. Heavy metals can seriously affect toluene biodegradation and regulate the abundance and diversity of microbial communities. SIP revealed a drastic difference in the community structure of active toluene degraders between the unpolluted and heavy metal-polluted soils. All SIP-identified degraders were assigned to nine bacterial classes, among which Alphaproteobacteria, Gammaproteobacteria, and Bacilli were shared by both treatments. Among all active degraders, Nitrospira, Nocardioides, Conexibacteraceae, and Singulisphaera were linked to toluene biodegradation for the first time. Notably, the type of active degrader and microbial diversity were strongly related to biodegradation efficiency, indicating their key role in toluene biodegradation. Overall, heavy metals can affect the microbial diversity and alter the functional microbial communities in soil, thereby influencing the removal efficiency of organic contaminants. Our findings provide novel insights into the biodegradation mechanism of organic pollutants in heavy metal-polluted soils and highlight the biodiversity of microbes involved in toluene biodegradation in compound-polluted environments.