Oncidium is an important fresh-cut flower in the market because of its unique flower pattern and brilliant color. The petals of Oncidium are highly susceptible to flower diversity. RNA extraction and transcriptome analysis were performed on the lateral petals of O. flexuosum ‘Honey Angel’ and variants with two lateral petals converted into lips to explore the molecular mechanism regulating the labialization of Oncidium lateral petals. A total of 45 525 415 high-quality reads were obtained from the sequencing results and 52 253 unigenes were identified. The seven databases of NR, Swissprot, PFAM, GO, NT, KO and KOG were used to annotate gene functions and annotated to 31 828, 23 174, 21 369, 21 367, 20 830, 10 523, 6465 unigenes. Upon expression comparison,3120 differential genes were obtained between O. flexuosum ‘Honey Angel’ and the mutant. A total of 1537 differentially expressed genes were annotated into three functional groups: biological processes, cellular components and molecular functions. KEGG functional enrichment analysis enriched 690 differentially expressed genes into different metabolic pathways, with the most genes enriched by metabolic pathway. To date, the study of lip formation in orchids has focused more on the MADS-box gene family, not only five significantly differentially expressed MADS-box genes were screened in this transcriptome data, but also other transcription factor such as NAC, TCP, MYB and WRKY that may be related to the lip formation in Oncidium were also discovered. RT-qPCR was used to verify the expression of key genes, and the quantitative results were consistent with RNA-seq data, most of the genes were highly expressed in the lip-like lateral petals, indicating that the genes may positively regulate the development of the lip of Oncidium. In summary, this study excavated a large number of key transcription factors involved in the variation of labialization in Oncidium, which would provide a certain reference for the study of the molecular mechanism and regulatory network of lip formation of orchid.