According to the description of Flora of China, the corolla of the normal Qinling stone butterfly is a twolipped structure (normal 23 type) with 2 upper lips and 3 lower lips, our group found a large number of artificially bred Qinling stone butterfly population Corolla variation type with twolobed upper lips and fourlobed lower lips (variants 24). In order to find out the reasons for the variation of Qinling stone butterfly petals, we used Illumina HiSeq 2500 highthroughput sequencing technology to sequence the transcriptome of the two different periods (buds and flowers) of the two flower types (normal 23 and variant 24) of Petrocosmea qinlingensis, and discover the differential genes involved in its flower development and explore the possible mechanism of floral variation. The results showed that: (1) compared with the NR database, a total of 52 677 Unigenes were annotated to the NR database, accounting for 46.25% of the total number of Unigenes, and the sequence homology with Dorcoceras hygrometricum was the highest (54.29%). (2) The results of GO enrichment analysis showed that the most significant GO terms for differential gene enrichment of normal 23 and variant 24 were the membrane classified by cellular component, the antiporter activity and enzyme inhibitor activity of molecular function class, transmembrane transport and negative regulation of catalytic activity of biological process, etc. The results of KEGG enrichment analysis showed that the most significant KEGG pathways for normal 23 and variant 24 differential gene enrichment were plant hormone signal transduction, fatty acid elongation, pentose and glucuronate interconversions, phenylpropanoid biosynthesis, sulfur metabolism, flavonoid biosynthesis, zeatin biosynthesis and other pathways. (3) The differentially expressed genes were screened and the 4 comparison groups were further analyzed by crosscomparison, and 6 genes that may be related to the development of P. qinlingensis flower organs were determined. They are PqMIF2, PqMYB340, PqMYB305, PqGATA12, PqCCD4 and PqZBED. qRTPCR verification found that its expression trend is consistent with the results of transcriptome sequencing analysis. This study provides valuable information for floral organ development, phylogeny and endangered mechanism of Petrocosmea qinlingensis.