Recent global climate change affects the living conditions of many plant and animal species on Earth. Capparis spinosa L. is a perennial xerophytic shrub with significant adaptability to arid environments and a candidate species for the prevention of soil erosion. However, its reference genome or large-scale full-length cDNA sequences are still lacking. Here, we applied a combination of second and third-generation sequencing technologies to sequence the full-length transcriptome in Capparis spinosa L. In total, 14.96 GB of clean reads were generated, including 828,518 reads of insert (ROI) and 370,258 full-length non-chimeric (FLNC) reads. We reported 216,240 consensus isoforms by transcript clustering analysis. After removing redundant reads, we identified 191,599 non-redundant isoforms of which 171,893 were coding isoforms. Through second-generation sequencing (SGS), we obtained 434 differentially expressed genes (DEGs) from samples collected under different temperatures for further analysis. Among these DEGs, we found 29 transcription factors belonging to seven different TF families in which CsMYB28 and CsMYB73 were up-regulated as the temperature rose. Overall, this is the first study to perform SMRT sequencing of full-length transcriptome of Capparis spinosa L. Our results will contribute to increasing interest for Capparis spinosa L as a candidate crop for future environmental challenges.