In the context of increasing global climate change, drought stress greatly affects the growth, yield and quality of medicinal plants. In this study, we analyzed the impact of drought stress on Scutellaria baicalensis Georgi (known as "Huang Qin") during critical growth stages, emphasizing the necessity for rational irrigation strategies in cultivation amidst global climate change. We conducted a pot experiment with well-watered (CK), leaf-extension stage (LES) drought stress (T1), and seed-ripening stage (SRS) drought stress (T2) treatments. We assessed root morphology, physiology, and active constituent contents at each stage and harvest. The results revealed significant reductions in root dry weight and active constituent yields under drought stress, particularly during the SRS. Compared with that in CK, the root dry weight significantly decreased by 48.87 % and 21.22 % during the LES and SRS, respectively, with SRS stress exhibiting a decrease of 11.43 % compared to LES stress at harvest. Moreover, active constituents like baicalin, baicalein, wogonoside, and wogonin also experienced significant yield reductions in T1 and even more in T2. Factor analysis revealed that both root dry weight, positively influenced by main root diameter, root surface area, and root volume (accounting for 64.74 % of total variance), along with active constituent content played a crucial role in determined the active constituent yields, with root dry weight being the major contributor. Therefore, this study underscores the importance of optimizing irrigation strategies in the cultivation of S. baicalensis. Ensuring water supply to mitigate severe drought (40 %FC drought stress), particularly during the later growth stage, is crucial for achieving high-yield and high-quality of S. baicalensis.