Microplastics (MPs) pollution is ubiquitous, causing serious ecological damage by threatening the growth and health of living organisms. This study investigated the vertical and horizontal distribution of MPs, MPs-heavy metals (MPs-HMs) accumulation, contamination assessment and microbial biodiversity in hyporheic sediments of different land-use types. MPs abundance in shallow sediments (0-30 cm) was significantly higher than that in deep sediments (30-60 cm), with fewer large MPs in the deep sediments. Blue, fiber, and <500 μm were the dominant MPs types, and polystyrene, polylactic acid, and polyvinyl chloride were the dominant polymers in the Beiluo River Basin. The average concentrations of HMs detected in MPs were all much higher than the same metals in the sediments. The pollution loading index of MPs was higher in areas with a greater proportion of anthropogenic land use, and MP-HM were present to varying degrees in the vertical distribution (PN>1). Critically, bacterial diversity of anthropogenic land use was smaller than that of natural land use. High MP-HM concentrations reduced the abundance of cyanobacteria, nitrospirota, acidobacteriota, and planctomycetota, whereas desulfobacterota, chloroflexi, myxococcota, actinobacteriota, and proteobacteria have developed tolerance to MP-HM. Overall, our findings contribute to the understanding of the relationship between different land-use types and the spatial distribution of MPs and MP-HM, which is critical to manage and mitigate the hyporheic zone pollution.