Amaranthus spp. are a group of strongly invasive and vigorous plants, and heavy metal phytoremediation using alien invasive Amaranthus spp. has been a popular research topic. In this study, the bioconcentration factor (BCF) and translocation factor (TF) of Amaranthus spp. were evaluated, focusing on the accumulation potential of cadmium (Cd) and lead (Pb) by plants from three different zinc mining areas, namely Huayuan (HYX), Yueyang (LYX), and Liuyang (LYX). The HYX area has the most severe Cd contamination, while the LYX area has the most apparent Pb contamination. The results showed that Amaranthus spp. had a strong Cd and Pb enrichment capacity in low-polluted areas. To elucidate the underlying mechanisms, we used high-throughput sequencing of 16S rRNA and internal transcribed spacer (ITS) regions to analyze rhizosphere bacterial and fungal communities in three areas. The results showed significant differences in the structure, function, and composition of microbial communities and complex interactions between plants and their microbes. The correlation analysis revealed that some key microorganisms (e.g., Amycolatopsis, Bryobacterium, Sphingomonas, Flavobacterium, Agaricus, Nigrospora, Humicola) could regulate several soil factors such as soil pH, organic matter (OM), available nitrogen (AN), and available phosphorus (AP) to affect the heavy metal enrichment capacity of plants. Notably, some enzymes (e.g., P-type ATPases, Cysteine synthase, Catalase, Acid phosphatase) and genes (e.g., ZIP gene family, and ArsR, MerR, Fur, NikR transcription regulators) have been found to be involved in promoting Cd and Pb accumulation in Amaranthus spp. This study can provide new ideas for managing heavy metal-contaminated soils and new ways for the ecological resource utilization of invasive plants in phytoremediation.