Microbial biomass phosphorus (Pmb) is an important P pool and its turnover can supplement the P pool in soil solution promoting plant productivity, and ubiquitously distributed alkaline phosphatase-encoding bacteria (PEB) containing the phoD gene mediate organic P mineralization. Yet, linkage between soil PEB and Pmb remains poorly understood, particularly in changing environments. Molecular and statistical tools were adopted in both environmental change simulation experiments and a field investigation to unveil the linkage between soil Pmb and PEB. Simulation experiments revealed that bacterial rather than fungal Pmb responded significantly to three types of environmental change (i.e., rainfall, acidification/alkalization, and warming), whereby higher Pmb content and P-cycling gene abundance were found under conditions of low environmental changes than of pronounced environmental changes. Pmb content was significantly positively correlated with phoD gene abundance in both simulated experiments and the field survey, thereby, specific bacterial genera (e.g., Stenotrophomonas) were notably correlated with Pmb. According to abundance and presence-absence identification of rare vs. abundant PEB, we found that rare rather than abundant PEB displayed a higher community diversity, closer phylogenetic clustering, stronger environmental restriction, and broader environmental breadth. In contrast, abundant PEB showed stronger species replacement and phylogenetic signals compared to rare ones. Rare and abundant PEB constituted stochasticity-governed community assemblages, and stochastic processes affected community assemblage of abundant PEB more than rare PEB. Our study extends our knowledge on a potential contributor of phoD gene to soil Pmb, and our findings reveal how rare and abundant PEB remain diverse and respond to changed environments.