Phase transitions in blue phase liquid crystals (BPLCs) have attracted significant attention from the technical perspective of BP orientation control and the theoretical perspective of analogs with crystalline solids. The phase transition phenomena in BPs significantly depend on the phase state before the transition. In this study, we focused on the cholesteric (Ch)–BPI phase transition and found that BPI crystals exhibited a square shape upon the phase transition from the uniformly oriented Ch phase to the BPI phase. This square crystal shape was common across three BPLC materials with different elastic constants, and the shape reflected the crystal axis. The in-plane crystal orientation correlates with the easy axis on the substrate surface, suggesting that the [011] axis tends to coincide with the easy axis. However, the easy axis has little effect on the crystal growth rate. Furthermore, scratches on the substrate surface promoted nucleation. Based on this behavior, it was demonstrated that the nucleation position and density could be controlled by intentionally disturbing the Ch orientation by locally changing the easy axis using photoalignment. This study focused on the anisotropic crystal growth of BPI, providing interesting insights into LC phase transitions and soft matter crystal growth. In addition, it offers techniques for the fabrication of large BPI crystals, contributing to the enhanced electrical and optical performances of BPLC devices.