In order to reveal the molecular mechanism of heat shock on ovule expansion, the global transcriptional profiles using RNA-seq were revealed based on the unfertilized ovules of watermelon under heat shock treatment. Total RNAs were extracted from the unfertilized ovules at 0 hour (A1), 4 hour (A3), 8 hour (A5), 12 hour (A7) and 24 hour (A8) post heat shock at 37℃, and then subjected for RNA-seq. Overall, 10093 differentially expressed genes (DEGs) were detected in the four pair-wise comparison groups (A3 to A1, A5 to A1, A7 to A1 and A8 to A1), including 4645 DEGs that were commonly detected at four comparisons. The cluster analysis of DEGs showed that the transcriptional reprograming of unfertilized ovules occurred after heat shock at 37℃ for 4 h, implying that the earlier response upon heat shock treatment. GO analysis showed that DEGs were mainly annotated in cell processes, cell parts and organelles, suggesting that heat shock may increase the activity of ovule cells. KEGG analysis revealed enrichments in amino acid metabolism, carbohydrate and sugar metabolism, plant hormone signal transduction and MAPK signaling pathway, which raises a putative impact on the development of unfertilized ovule. In addition, it was found that changes in the expression of DEGs related to heat shock proteins, plant hormones and embryo development under heat stress may be important in inducing unfertilized ovule development, which provides preliminary insights for future unlocking the molecular mechanism of heat shock development of unfertilized ovules in watermelon.