In this study, the four-layer h-BN/h-BN and Gr/Gr interface systems were employed to investigate the effects of the atomic relaxation on the DFT-calculated friction properties by using the LICP-FPHTC-Platform based on the DFT methods. Atomic relaxation means that the cell lattice is optimized and then relaxed again for complete fixation of the top and bottom atoms. Atomic non-relaxation means that only lattice optimization is performed. The results show that the DFT-calculated friction properties without the atomic relaxation are creditable at larger interface distances, but the atomic relaxation should be considered at the interface distance is less than a certain distance. Further analysis of the atomic configuration and electronic structure shows that spontaneous motion of atoms is the main reason for the decrease of DFT-calculated frictional force and the in-plane atomic relaxation can reduce the interface interaction. This work can provide references for the selection of DFT calculation schemes to study the material friction properties.