The weathering of phosphorus-bearing mineral powder (PBMP) and calcium phosphate (CP) by Aspergillus niger was compared, and the mechanism involved was analyzed for the comprehensive utilization of PBMP. The concentration of water-soluble phosphorus (WSP), Mg2+, and Ca2+ at different culture times, microstructures of particles, and mineral compositions was examined by ultraviolet-visible spectrometer (UV), atomic absorption spectrometry (AAS), scanning electron microscopy (SEM), and X-ray diffraction (XRD). Results showed that the change in the concentrations of WSP, Mg2+, and Ca2+ were related to the growth of A. niger and the different mineral compositions. Compared with CP, PBMP was weathered harder by fungi. Traces of the weathered mineral were found through SEM. CP not only showed traces of erosion damage but also appeared as a rhombohedron-like substance. The XRD test indicated that the weathering minerals can form water calcium oxalate. Further analysis revealed that the mechanism of PBMP and CP weathering by A. niger was the collaborative result of mycelium biomechanical effects and the acid-soluble role of acidic metabolites. The phosphorus dissolution rate of PBMP after 20 d was 46.83%, whereas that of CP after 12 d was 91.01%. The findings of this study are significant to the effective use of waste PBMP and to the exploitation of low-grade phosphate rock resources.