It is of vital importance to understand the interfacial thermal conductance between the high thermal conductivity fillers and the phase change thermal energy storage materials in order to enhance the energy storage efficiency. The interfacial thermal conductance across low-dimensional hexagonal boron nitride layers (h-BN) and n-octadecane was calculated with reverse non-equilibrium molecular dynamics methods in this paper. The influences of size effect, molecular arrangement of n-octadecane, layer number of h-BN as well as the defects modified with various functional groups on the interfacial thermal conductance within the temperature range from 273.15 to 373.15 K were investigated, respectively. The results showed that the interfacial thermal conductance of all systems increase with rising temperature and the size effect is inconspicuous. And systems with n-octadecane molecules parallel to the h-BN surface possess the highest interfacial thermal conductance with respect to the vertical and amorphous arrangements. In addition, the interfacial thermal conductance will reduce when the layer number of h-BN increases. In terms of the effect of defects, the systems with h-BN containing the defects modified with hydrogen atoms, i.e., lighter atom, possess higher interfacial thermal conductance. At last, for interpreting deeper mechanism, the vibration power spectrum of the velocity autocorrelation function and the components in different directions were also calculated.