Pennisetum setaceum ‘Rubrum’ is an ornamental herb with purple leaves, and it is widely used in the construction of landscaping. However, the current next generation sequencing (NGS) transcriptome information is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts. What’s more, the molecular mechanisms of anthocyanin accumulation have not been thoroughly studied. In this study, we used PacBio full-length transcriptome sequencing combined with NGS sequencing technology to conduct transcriptome analysis on leaves showing different colors at different stages to clarify the molecular mechanism involved in the color change of P. setaceum ‘Rubrum’. A total of 280,413 full-length non-chimeric reads (FLNC) sequences were obtained based on single-molecule long-read sequencing technology. We obtained 140,633 high quality (HQ) transcripts and 2,683 low quality (LQ) transcripts and identified 5,352 alternative splicing (AS). In addition, a total of 93,066 ORFs, including 57,457 full open links and 2,910 lncRNA sequences were screened out. Furthermore, a total of 10,795 differentially expressed genes were identified. Gene ontology (GO) cluster and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the underlying mechanism of anthocyanin accumulation. In this study, to our best knowledge, we provided the full-length transcriptome information of P. setaceum ‘Rubrum’ for the first time. The underlying mechanism of anthocyanin accumulation in P. setaceum ‘Rubrum’ was further discussed based on the newly generated transcriptome data. The information will not only facilitate the gene function studies but also pave the way for future breeding projects of Pennisetum setaceum .