Background: Streptococcus mutans (S. mutans) is the primary etiological agent of dental caries. Probiotic therapy, such as with Lactobacillus acidophilus (L. acidophilus), represents a promising strategy for caries prevention, partly through co-aggregation with S. mutans via bacterial surface adhesins. However, the specific S. mutans adhesion proteins bound by probiotics remain largely unexplored due to challenges including undefined bait proteins, high background noise, and complex membrane structures. Results: We developed a biomimetic proteomic nanoplatform that integrates L. acidophilus membrane-modified nanoparticles with quantitative proteomics to capture and identify S. mutans surface adhesion proteins. This platform enables high-throughput, affinity-based enrichment without predefined bait proteins. Using this approach, we identified several known adhesion-related proteins alongside previously undefined candidates. These findings were validated through subsequent gene knockout experiments. Conclusions: This study innovatively combines membrane-modified nanotechnology with quantitative proteomics to elucidate interbacterial adhesion proteins. The established platform provides a novel methodological approach for investigating bacterial effector proteins and bacteria-bacteria interactions.