In this study, using heat tolerance line 996 and heat sensitive line 4628 as materials, we performed microarray analysis on the RNA extracted from the 5-6 stage young panicles of the two rice varieties treated with 40 ℃ for 0 min, 10 min, 20 min, 60 min and 2 h. The results showed that the differentially expressed genes of the two varieties were significantly enriched in phenylpropane biosynthesis, heat shock protein, tetratricopeptide repeat, and processes related to abiotic stress. In addition, heat tolerance line 996 differentially expressed genes were also significantly enriched in cytochrome P450. The heat sensitive rice 4628 differentially expressed genes were significantly enriched to pentatricopeptide repeat. With the results from this study, we could conclude that heat tolerance rice 996 may improve its own heat tolerance due to the differential expression of cytochrome P450 family genes, and heat sensitive rice 4628 may be due to the existence of PPR gene to affect its own stress resistance. The differentially expressed genes in the heat tolerance line 996 and heat sensitive line 4628?? provided information for further heat resistant gene identification and clarification of the heat resistant mechanism.