Aiming at the pilot contamination problem in massive Multiple-Input Multiple-Out (MIMO) systems, a dynamic pilot allocation scheme based on graph coloring was proposed. To allocate pilot more reasonably and mitigate pilot contamination, firstly, an edge-weighted interference graph based on cooperation among cells was constructed to describe the strength of pilot contamination among multi-cell users, whereby two users in different cells were connected by a weighted edge. Then, based on the traditional graph coloring theory, pilot resources were allocated preferentially to users who were heavily polluted by the characteristics of different weighted edge for connected users. The theoretical analysis and simulation results show that, compared with existing distributed pilot allocation scheme, the proposed pilot allocation scheme can reduce the inter-cell interference and enhance the uplink achievable sum rate by considering pilot reuse of all cells and centralized pilot allocation mechanism based on graph coloring.