The effects of heavy metal contamination on soil biomes have been of considerable interest. However, the effects of heavy metal pollution on the interactions between soil multi-trophic biota in soil food webs and the regulatory mechanisms still need more research, especially in different soil situations. This study examined the impact of heavy metal contamination on soil micro-food web in two distinct soil resource availability situations. Under low soil resources availability situation, heavy metals mainly affected the community structure of soil bacteria and nematodes, with the number of edges of the bacterial network and network complexity reduced by 60.5% and 187%, respectively. In addition, the presence of heavy metals led to a significant reduction in the energy flow from soil resources to bacterivores in the nematode food web. For micro-food webs, heavy metal contamination increased the network average degree by 18.8% and 11.56% in the low and high resource availability situations, respectively. However, in high soil resource availability, heavy metal contamination decreased micro-food web stability and eased competitive relationships among multitrophic organisms and increased microbial carbon limitation and mitigates nitrogen limitation. In low soil resource availability, it increased network stability and shifted relationships among micro-food web organisms from cooperative to competitive and decreased microbial carbon limitation and aggravated nitrogen limitation. This study offers new research insights into the feedback discrepancy between resource availability and pollution stress from the perspective of multitrophic level interactions and further deepens the understanding of the environmental impacts of heavy metal pollution at the ecosystem level.