Understanding the crystal structure of WO3 is essential for optimizing its photoelectrochemical performance. This study comprehensively analyzes the structural characteristics of WO3 during synthesis and investigates their correlation with photoelectrochemical activity. Structural analysis, incorporating annealing procedure and WO3 thickness, identifies a blend of hexagonal, monoclinic, and orthorhombic phases within WO3 array. Specifically, detailed analysis reveals a predominance of monoclinic WO3 phase alongside the orthorhombic WO3 phase, both of which are commonly characterized by their monoclinic structure. Three-dimensional thermomechanical simulations using the finite element method reveal that thermal displacement in WO3 layers increases with thickness during the thermally induced synthesis process. These results highlight a direct correlation between WO3 thickness, thermal displacement, and phase transition, with thicker layers favoring the transformation from orthorhombic to monoclinic structures due to increased thermally induced deformation. The heightened monoclinic structure, which possesses lower symmetry than the orthorhombic structure, induces more defect sites, suggesting increased donor density. Notably, the monoclinic-dominated WO3 exhibits superior performance under UV-visible irradiation in 0.5 M NaCl. Furthermore, the WO3 array demonstrates over 85% Faradaic efficiency for chloride oxidation, indicating preferential selectivity over oxygen evolution reaction in 0.5 M NaCl. This study emphasizes the pivotal role of the crystal structure of WO3 in achieving efficient photoelectrochemical seawater splitting.