To resolve intra-cell pilot collision in crowded massive multiple-input multiple-output systems, a new pilot random access protocol, called strongest-user collision resolution combined graph-based pilots access (SUCR-GBPA), is proposed. This protocol allows all failed user equipments (UEs) to randomly select a pilot from the pilots that are not selected by any UE in the initial step. By exploiting the characteristic that the channel responses between UEs and the base station are invariant within the coherence time, a bipartite graph is established where active UEs and selected pilots are considered variable nodes and factor nodes, respectively. Based on this bipartite graph, the successive interference cancellation algorithm is employed to estimate the channel response of each UE. Finally, utilizing the and-or tree principle, we analyze the performance of the proposed SUCR-GBPA protocol, including the maximum number of the tolerable active UEs, the minimum number of the required pilots, uplink throughput, and the mean-square-error performance of the SUCR-GBPA channel estimation. Simulation results demonstrate that, compared with the SUCR protocol, the proposed SUCR-GBPA protocol significantly improves the uplink throughput and provides accurate estimation on the channel response at the same time.