Alternative splicing (AS) regulates mRNAs at the post-transcriptional level to affect both their amounts and the protein function. However, little is known about the roles of AS in regulation of biosynthesis of amino acids, flavonoids, and volatile compounds in tea plants. In this study, we used Iso-seq and transcriptome deep sequencing (RNA-seq) to identify AS events, and analyzed the expression of respective mRNAs in tea plants under drought (DS), heat stress (HS), and their combination (HD). By RT-PCR, we validated the AS events in nine genes involved in the biosynthesis of amino acids and flavonoids. The genes accumulating AS transcripts under DS, HS, and HD conditions included those encoding for anthocyanidin reductase (ANR), dihydrofavonol-4-reductase-like (DFRA), and chalcone isomerase (CHI). Similarly, genes directly or indirectly involved in the biosynthesis of volatile compounds such as lipoxygenase (LOX), terpenoid/terpene synthase (TPS), and 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) also had AS events. Our study revealed that AS might specifically regulate the biosynthesis of amino acids in tea plants under stressful conditions. Moreover, we suggest that the AS events within the ANR and DFRA transcripts might play an important role in the regulation of flavonoid biosynthesis under DS, HS, and HD conditions. This study improved our understanding of the genetic drivers of the changes in the content of bioactive ingredients of tea plants subjected to abiotic stresses.