Objective To address the limitations of the traditional fractionation process of Camellia oleifera seed oil, a novel molten layer crystallization process based on crystallization kinetics theory is developed.Methods Using crude C. oleifera seed oil as the raw material, the metastable zone width and nucleation induction period are investigated by laser scattering technology, while the thermal properties of its high-melting-point constituents are characterized by differential scanning calorimetry (DSC). Based on these findings, a gradient cooling and fractionation process for molten layer crystallization is designed. Subsequently, a comparative analysis is conducted to evaluate the fatty acid profile, lipid composition, isothermal thermal properties, and crystallization kinetics of C. oleifera seed oil before and after fractionation.Results The metastable zone width of C. oleifera seed oil significantly expands with increasing cooling rate, and the nucleation induction period at -20 ℃ represents the critical transition point for the nucleation kinetics. DSC analysis reveals that the high-melting-point constituents possess a solidification point of -17.8 ℃ and a melting point of -6.8 ℃. Following fractionation, the saturated fatty acid content in C. oleifera seed oil increased markedly to 26.99%. Furthermore, lipid chain lengths ranging from L50 to L54 and low-unsaturation class u2 lipids are selectively enriched. Crystallization kinetics analysis indicates a shift in the primary crystallization mechanism from homogeneous nucleation in the C. oleifera seed oil to heterogeneous nucleation.Conclusion Crystallization kinetic parameters, such as metastable zone and induction period, can effectively guide the crystallization and fractionation process of the molten layer in C. oleifera seed oil production.