Withering leads to the formation of high-quality flavor in black tea. This study investigated the effects of natural withering (NW), sun withering (SW), and warm-air withering (WW) on the flavor compounds of withered leaves by using target metabolomic and transcriptomic approaches. The results revealed that 4282, 4770, and 1246 differentially expressed genes (DEGs) were identified in the NW, SW, and WW samples, respectively. The expression of DEGs involved in volatile compound and flavonoid biosynthesis was the highest in the WW sample, which may be the main reason for the significant increase in volatile compound and catechin contents in the WW sample. The withering methods mainly affected the contents of non-proteinaceous amino acids, such as theanine. Withering methods significantly affect the expression levels of DEGs involved in metabolic pathways; this provides a systematic explanation for flavor formation in black tea.