Abstract Molten salt synthesis offers a versatile platform for catalyst fabrication, however, the mechanistic understanding of crystallization within molten salt system remains limited, hindering the rational tailoring of composition and morphology of the catalysts. Here, the intrinsic mechanism of molten salt‐mediated crystal growth is revealed, which is exemplified by the growth of poly(heptazine imide) (PHI) and poly(triazine imide) (PTI). It is demonstrated that the solidification state of the salt template determines the structural and morphological transformation. By controlling the cooling program, the synthesis of PHI/PTI homojunctions with controllable components and morphologies is realized. Furthermore, the well‐defined homojunction composed of PHI nanorods and PTI hexagonal prisms is obtained, with unsaturated Ni−N 2 sites selectively anchored on PHI via ion exchange. The resulting Ni‐decorated homojunction follows a Z‐scheme charge transfer mechanism, which significantly promotes charge separation and maximizes the redox ability. When applied to photocatalytic CO 2 reduction, the homojunction catalyst reaches a CO production rate of 121 µmol g −1 h −1 , which is 3.6 and 7.6 times those of pure PHI and PTI, respectively. This work deepens the understanding of molten salt‐mediated crystallization and demonstrates a viable pathway for fabrication of high‐performance catalysts through crystallization manipulation.