Pilot sequences are inevitably multiplexed in different cells, resulting in pilot pollutions. The interference caused by pilot pollution does not decrease as the number of base station antennas increases. Pilot decontamination is one of the main reasons, which limits the performance of massive Multiple-Input Multiple-Output (MIMO) systems. To reduce the effect of pilot pollution, pilot assignment scheme with time-shift joint space partitioning is proposed, which is based on time and space domains. The pilot decontamination can be mitigated by reducing the number of reused times of the pilot sequence in two directions. We also derive the achievable uplink users access rate and Signal-Interference-Noise Ratio (SINR)in the system. The simulation results show that the proposed scheme can effectively reduce pilot pollution and improve the system performance.