In this study, two different hybrids of Easter lily (Lilium longiflorum), obtained from two cross combinations, along with their four parents were sequenced by high-throughput RNA-sequencing (RNA-Seq) to find out differentially expressed gene in parent-hybrid combinations. The leaf mRNA profiles of two hybrids and their four parents were RNA-sequenced with a view to identify the potential candidate genes related to plant height heterosis. In both cross combinations, based to morphological traits mid-parent heterosis (MPH) was higher than high-parent heterosis (HPH) for plant height, leaf length, and number of flowers whereas HPH was higher than MPH for flowering time. A total of 4,327 differentially expressed genes (DEGs) were identified through RNA-Seq between the hybrids and their parents based on fold changes (FC) ≥ 2 for up- and ≤ -2 for down-regulation. Venn diagram analysis revealed that there were 703 common DEGs in two hybrid combinations, those were either up- or down-regulated. Most of the commonly expressed DEGs exhibited higher non-additive effects especially overdominance (75.9%) rather than additive (19.4%) and dominance (4.76%) effects. Among the 384 functionally annotated DEGs identified through Blast2GO tool, 12 DEGs were up-regulated and 16 of them were down-regulated in a similar fashion in both hybrids as revealed by heat map analysis. These 28 universally expressed DEGs were found to encode different types of proteins and enzymes those might regulate heterosis by modulating growth, development and stress-related functions in lily. In addition, gene ontology (GO) analysis of 260 annotated DEGs revealed that biological process might play dominant role in heterotic expression. In this first report of transcriptome sequencing in Easter lily, the notable universally up-regulated DEGs annotated ABC transporter A family member-like, B3 domain-containing, disease resistance RPP13/1, auxin-responsive SAUR68-like, and vicilin-like antimicrobial peptides 2-2 proteins those were perhaps associated with plant height heterosis. The genes expressed universally due to their overdominace function perhaps influenced MPH for greater plant height- largely by modulating biological processes involved therein. The genes identified in this study might be exploited in heterosis breeding for plant height of L. longiflorum.