To explore the mechanism of how a high general combining ability (GCA) parent contributes to heterosis, we used Illumina RNA-Seq technology to characterize the transcriptome of F1-hybrid rice leaves. We found that the global transcriptome of these F1 hybrids was downregulated rather than upregulated compared with their parents. Approximately half of the total of genes exhibited either monoallelic or preferential allelic expression. Monoallelic genes were distributed in clusters and were reprogrammed in the F1 hybrids. This reprogramming of monoallelic genes could be an alternative way to modulate the global transcriptome in F1 hybrid rice. Our results suggest that allele-specific expression downregulates the global transcriptome in hybrid rice and could be a possible molecular mechanism for general combining ability.