Woody plants must acclimate to environmental stresses, including soil salinity, for proper growth and development. Microtubule reorganization supports plant survival in saline-rich soils, but the underlying molecular mechanism in tree species remains unclear. In this study, we identified a salinity stress response mechanism in hybrid poplar seedlings. This mechanism involves regulation of microtubule dynamics by the microtubule-associated protein PLASMA MEMBRANE–ASSOCIATED CATION BINDING PROTEIN 1a (PagPCaP1a). Salinity stress induced PagPCaP1a expression and phase separation of PagPCaP1a protein to form PagPCaP1a condensates in a calcium-dependent manner. The formation of PagPCaP1a condensates was partially driven by the VEEEKK motif within the carboxyl terminus of the protein, which rapidly depolymerizes microtubules under salinity stress. Our study reveals that the liquid-liquid phase separation of PagPCaP1a represents an additional regulatory layer for microtubule depolymerization, and we propose an effective strategy to manipulate the phase separation of PagPCaP1a to improve plant stress tolerance.