To reduce the high cost caused by steam sterilization of fermentation substrates and equipments in mesophilic solid-state fermentation of rapeseed meal (RM), a thermophilic protease-producing strain RM-2 from RM was isolated and employed in thermophilic solid-state fermentation of unsterilized RM for polypeptide preparation. The isolate was identified as Geobacillus stearothermophilus by appearance of colonies and microscopic observation as well as 16S rDNA sequencing. The highest yield of polypeptide (9.67%) was obtained by RM-2 at 50% moisture content, 55 °C and 24 h fermentation time. Analysis of microbial community diversity in fermented RM revealed Geobacillus stearothermophilus as dominant strain inhibiting most mesophilic microorganisms. Thermophilic solid-state fermentation on RM improved the yield of rapeseed polypeptide, as well as the utilization rate of substrate. The application of this technology (thermophilic solid-state fermentation) would be environmentally friendlier and energy-saving to industry.