In vitro gynogenesis is an important tool used in haploid or homozygous double-haploid plant breeding. However, because of low repeatability, embryoid induction rate and quality, the molecular mechanisms remain poorly understood. Heat shock treatment can promote the transformation of the gametophytic pathway into the sporophyte pathway, which induces the occurrence of haploid. In this study, unfertilized ovaries were heat shocked for 0 h (A0) before flowering and for 0 h (A1), 4 h (A3), 8 h (A5), 12 h (A7), and 24 h (A8), respectively, at 37°C at the first day of the flowering stage. The ovule enlargement rate was increased from 0％ at 25°C to 96.8％ at 37°C (24 h treatment). Thus, we aimed to investigate the gene expression patts in unfertilized ovules of watermelon after different periods of heat shock by using RNA-Seq technology. The results showed that compared with A3, A5, A7, and A8, the biosynthesis of amino acid, glycine, serine and threonine metabolic pathways in A1 has changed significantly. This indicated that heat shock treatment affected the synthesis and transformation of amino acids during ovule expansion. The transcriptome data suggested gene expressions of ovule growth were significantly changed by heat-specific influences. The results provide new information on the complex relationship between in vitro gynogenesis and temperature. This provides a basis for further study of the mechanism of heat shock affecting the expansion of watermelon ovule.