Salvia splendens is a perennial, ornamental herbaceous flower that is widely cultivated as a bedding plant in gardens. The development of novel S. splendens cultivars and investigating the relevant molecular mechanisms are of great significance. In this study, RNA-sequencing and real-time PCR methods were used to analyze the possible molecular mechanism of S. splendens mutant, SX919M. From the wild-type S. splendens 919CK, we firstly selected a natural mutant, SX919M, which displayed multiple branches, clustered spheroids, and radial symmetrical inflorescence with higher numbers of calyces, ovules, stamens, and perianth tubes. Further, the RNA-seq was used to identify the differentially expressed genes (DEGs) in the mutant which included a total of 3568 upregulated and 3290 downregulated unigenes. We further observed that the indole alkaloid biosynthesis pathway showed the highest DEG enrichment, which was supported by a significant increase in the IAA content in mutant SX919M. In addition, we validated three DEGs, namely, CL2200.Contig2_All encoding methyl IAA esterase, CL12462.Contig1_All and CL12462.Contig2_All, which encoded strictosidine synthase, upregulated in mutant SX919M. We selected a novel S. splendens germplasm SX919M with a high ornamental value and determined that the upregulation of IAA biogenesis may be associated with its development.