Introduction Drought stress severely limits the survival and growth of Pinus tabuliformis seedlings during afforestation. However, the molecular mechanisms coordinating organ-specific responses across diverse geographical provenances remain inadequately characterized.Methods This study investigated the dynamic drought responses of two provenances of P. tabuliformis, originating from semi-arid (HLH) and semi-humid (SL) regions, through a time-course drought and rewatering experiment. Integrated transcriptomic and metabolomic analyses of roots and leaves revealed a clear functional specialization between these organs.Results Roots primarily initiated signal transduction and osmotic adjustment, whereas needles were predominantly engaged in minimizing water loss through transpiration. Notably, the HLH provenance demonstrated a rapid-response plasticity strategy, while the SL provenance exhibited a highly dynamic defensive strategy. Several key candidate genes, including Pt2G21940, Pt1G23820, and Pt5G10920, were identified. Furthermore, gene-metabolite correlation networks underpinning the dynamics of proline, jasmonic acid, and flavonoid metabolism were delineated.Discussion These findings provide a molecular foundation for deciphering the drought resistance mechanisms in P. tabuliformis and offer valuable genetic targets for breeding drought-tolerant conifers.