Intrinsic mosaic structures composed of distinctive stacking domains separated by domain walls (DWs) show the potential to regulate many outstanding properties of van der Waals layered materials. A comprehensive simulation at the atomic scale is performed to explore how the lattice/twist mismatch and the interlayer interaction influence the mosaic configuration from the incommensurate Moiré pattern to commensurate mosaic structures by adapting a complex amplitude version of the phase field crystal method. It is found that after an incommensurate-commensurate transition occurs, the topology of the mosaic structure indicated by different domain wall (DW) patterns can be drastically changed. An experimentally observed intriguing spiral domain wall (SDW) network is revealed as result of the emergent mixed dislocation driven by minimizing the elastic and interlayer energies in the presence of both lattice and twist mismatches. The transition process from a herringbone domain wall (HBDW) network to a SDW network is also simulated, elucidated by a dislocation reaction and in good agreement with the experimental observations.