Jatropha curcas is a woody perennial oil plant of the family Euphorbia, whose seeds contain high oil content (30-40%), and is considered as a potential renewable resource plant. However, few female flowers and low seed yield of J. curcas severely limit its application in agricultural production. Jasmonic acid (JA) is an important plant hormone, which plays important roles in flower development. To investigate the role of JA in flower development, the changes of transcriptome in the early inflorescence buds of Jatropha 24 h after treatment with 1.0 mM JA were detected using second-generation high-throughput sequencing technology. The results showed that 1259 genes were up-regulated expression and 695 genes were down-regulated expression in the inflorescence buds treated with JA, among which 10 orthologous genes of Arabidopsis floral transition genes, 8 orthologous genes of Arabidopsis floral organ development genes and 18 orthologous genes of Arabidopsis JA synthetic and signaling transduction pathways exhibited significantly changed expression, but the phenotype of floral organs was normal. GO annotation of differentially expressed genes (DEGs) showed that genes in the “responding to jasmonic acid” functional category are enriched in the up-regulated DEG group, indicating that the signaling pathways responding to the exogenous JA application are present in Jatropha. Moreover, after JA treatment the expression of JcFUL, JcSRS, JcSEP1, JcAGL61, JcWOX1, JcTPR4 and JcSEU genes related to floral organ development were down-regulated, but floral organ phenotype was normal, indicating that the down-regulated expression of these genes is not sufficient to alter floral organ phenotype in Jatropha. These results provide valuable information for analyzing the role of jasmonic acid in the regulation of floral development of Jatropha.