Nucleic acid delivery in hard‐to‐transfect macrophages have attracted increasing attention in diverse applications such as defence against bacterial infection. Regulated by microenvironments in specific applications, macrophages have a heterogenous nature and exist in different phenotypes with diverse functions, e.g., pro‐inflammatory and anti‐inflammatory. However, it is not clear whether macrophage phenotype affects nucleic acid delivery, and which one is harder to transfect, and the design of nucleic acid carriers in harder‐to‐transfect macrophage phenotypes is largely unexplored. Herein, it is first revealed that nucleic acid delivery efficacy in macrophages is influenced by phenotype: IL‐4‐treated “M2‐like” macrophages with suppressed mammalian target of rapamycin complex 1 (mTORC1) levels are harder‐to‐transfect than “M1‐like” macrophages for mRNA and DNA. This knowledge is then translated to the purpose‐design of gene delivery carriers for harder‐to‐transfect M2 phenotype macrophages dominant upon bacteria immune evasion. By loading chloroquine in tetrasulfide bond‐containing organosilica nanoparticles, the resultant composite promotes macrophage M2 polarization to M1 and increases mTORC1 levels for enhanced translation. The design is demonstrated in vitro and in vivo for pathogenic Escherichia coli (E. coli) and methicillin‐resistant Staphylococcus aureus (MRSA) infections. It is expected that the findings may provide new knowledge and gene delivery solutions in other applications where the M2 phenotype macrophage is dominant.