The technology of atomic layer deposition has been used to improve the lifetime of the microchannel plate-photomultiplier tube (MCP-PMT) effectively and makes MCP possible to choose to coat different potential emissive materials on the internal surface of the MCP channels in the future. However, it is still an open question to what extent the secondary electron emission (SEE) yield properties of the emissive materials influence the behavior of the ALD-coated MCP. In this work, the dependences of the gain and timing performance on the SEE yield properties were assessed by using the Monte Carlo and particle-in-cell methods. We established the three-dimensional MCP single channel model in Computer Simulation Technology (CST) Particle Studio. Three important secondary electron emissions, the backscattered, rediffused and true SEEs, were discussed numerically based on the probabilistic model. The secondary electron cascade processes in the MCP single channel were simulated. The simulation results indicate that the opportunities for improving the gain of the ALD-coated MCP by improving the SEE yields corresponding to the incident energies of 0 eV–100 eV. The backscattered and rediffused electrons are found to have strong effects on the gain and timing performance of the MCP. Although the higher the SEE yield the higher the MCP gain, the drawback is the extremely high SEE yield will make the MCP saturated prematurely and degrade the time resolution. The simulation results will be used to guide the design and selection of emissive material for ALD-coated MCP development. © 2021 Elsevier B.V.