Bilayer graphene has been a subject of intense study in recent years. We extend a structural phase field crystal method to include an external potential from adjacent layer(s), which is generated by the corresponding phase field and changes over time. Moreover, multiple layers can be added into the structure. Using the thickness of the boundaries between different stacking variants of the bilayer structure as the key parameter, we quantify the strength of the adjacent layer potential by comparing with atomistic simulation results. We then test the multiple graphene structures, including bilayers, triple layers, up to 6 layers. We find that besides the initial conditions, the way of new layers added into the structure will also affect the layout of the atomic configuration. We believe tour results can help understanding the mechanism of graphene structure consists of more than one layer.