Modifying the bacterial surface through grafting functional nanoparticles is a common strategy for programing bacteria. At this moment, the targeted nanoparticles face a dilemma of no multifunctional structure, high toxicity, and weak chemical driving forces, which restrict the broad practical applications. Like a multistage booster of a rocket, we propose a multistage covalent self-assembly strategy to protect, expand, and control the encapsulated shells of microbial cells via biocompatible hyper-cross-linked polymer nanoparticles (Bio-HCP NPs) with internal porosity and surface functional groups. The bacterial surface is enhanced with rich amino groups up to 1010 per cell for specifically grafting nanoparticles. The arming bacteria after first-stage assembly can complete biocatalysis in a highly toxic environment, and as-prepared polymer aggregates (6-20 μm) after third-stage assembly can be accurately counted in an aerosol environment. This nanoparticle encapsulation exhibits strong cell viability from pollutants and specificity from impurity particles, holding promise for various complex application scenarios.