In order to investigate the relationship between the RNA structure and thermal stability, we used real-time PCR method to survey the degradation information of Bombyx mori larvae inter reference gene RNA treated with 70 °C to 90 °C. The results showed that there were some relativities between the whole thermal stability RNA and the GC contents. The whole RNA displayed prominent degradation above 70 °C. The amplification length of the two inner reference genes were 147 bp and 150 bp, respectively, and the GC content were 59.184% and 44.667%, respectively. The risdual ratio was 67.712% and 50.849%, respectively. These results explained that there were negative correlation between the degradation rate and the GC contents. This study reported the correlation between the degradation rate and the GC contents of inner reference gene, providing the references for studying the RNA thermal stability and related molecular biology research.