Mg-bearing silicate minerals are very important natural resources, which being developed and used widely by the traditional chemical methods at home and abroad. While microbial release of magnesium and silicon from silicate minerals has been reported rarely. This paper mainly studied the weathering of the serpentine and olivine by Aspergillus fumigatus TH003 through the methods of shake culture and control groups. The concentration of Mg2+ and Si in the first 5, 10, 20, 30d, the changes of the value of pH, metabolites and morphological have been analysed by the ICP-OES, GC-MS, SEM and TEM. The results showed the change of the concentration of Mg2+ and Si is related to the growth of the Aspergillus fumigatus, and the concentration of Mg2+ in the samples of serpentine is two times of that in the samples of olivine, which means olivine is harder weathered than serpentine by the Aspergillus fumigatus. It also found some acidic organic substances produced in the process of microbe-mineral interaction which have some effects on the weathering of mineral. The traces of the mineral weathered have been found by the SEM and TEM. Above analysis confirmed the mechanisms of microbe-mineral weathered: acid-soluble role, parcels of mycelia and mineral, adsorption and absorption, mechanical action, as well as the role of synergy above. The results can provide some basic information for studying the process and mechanism of fungi-mineral interaction, and for the microbial development and use of serpentine and olivine in industry.