The increasing intensity, frequency, and duration of drought pose a threat to the survival of some tree species worldwide, directly damaging the carbon sequestration capacity of forest ecosystems. Understanding the response mechanisms of trees to drought stress is particularly important. In this study, a drought stress regulatory network in Betula platyphylla (birch) was established by observing the changes in the root transcriptome at different drought stress time points (0, 3, 6, 24, 48, and 72 h), and a potential drought-resistant WRKY53 transcription factor was identified. The overexpression of BpWRKY53 (OE-BpWRKY53) in birch enhanced drought tolerance. Yeast one hybrid (Y1H), electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation-PCR (ChIP-PCR), and dual-luciferase (dual-LUC) assays confirmed that BpWRKY53 positively activated BpCHS3 and BpCHSy expression by binding to the W-box in their promoter, consequently increasing the flavonoid content in birch. Exogenous application of flavonoids enhances the drought tolerance of birch. BpMAPK3-mediated phosphorylation of BpWRKY53 at Ser201 enhances its ability to regulate the expression of BpCHS3 and BpCHSy. Collectively, these results provide insights into the mechanism underlying drought-induced flavonoid biosynthesis through the transcriptional regulation of BpCHS3 and BpCHSy mediated by BpWRKY53.