To elucidate the underlying mechanism of crystallization processes of n-alkane mixtures, molecular dynamics simulation is used to assess the effect of the morphology on thermal conductivity. Binary mixtures of n-eicosane and n-triacontane with different molecular number ratios are solidified following two approaches: the surface potential route and the free surface route. There exists a marked discrepancy of the orientation factor of the resulting solid n-alkane molecules following the imposed surface potential and the free surface routes corresponding to observed layered systems and random ordering of molecular chains, respectively. In addition, the thermal conductivities of the n-alkane mixtures are evaluated using non equilibrium molecular dynamics. The results suggest that the orientation factor of the molecular system greatly impacts the thermal transport of n-alkane mixtures at the nanometer scale, with a negligible influence of the number ratio of n-triacontane. Moreover, the solid ratio plays a significant role on the thermal conductivity for low orientation factor systems by adjusting the number of thermal interfaces of the entire molecular system.