Microchannel plate-photomultiplier tubes (MCP-PMTs) with high dynamic ranges and strong outputs are still challenges for the future inertial confinement fusion (ICF) studies aiming at detecting the large-scale intens ities of the radiation pulses. In this paper, to investigate the influence factors of the gain nonlinearity causing high-linearity limits of the MCP-PMTs, three-dimensional MCP channel models were built in Computer Simulation Technology (CST) Particle Studio. The Monte Carlo and particle-in-cell methods were carried out to simulate the electron cascade processes in the channels of the MCPs. The dependences of MCP gain nonlinearity on the number of incident electrons, operating voltage, and secondary electron emission (SEE) yield properties were studied. The gains obtained by the simulations for the conventional one-stage and two-stage MCPs are in good agreement with the available experimental data, which verifies the reliabilities of the three-dimensional MCP models. The simulation results show that the gain of the MCP single channel decreases as the number of incident electrons increases due to the space charge effects. The higher operating voltage and SEE yield of the MCP, the faster the gain deteriorates. To mitigate the gain saturation effect of MCP single channel, a novel structural design of MCP-PMT has been proposed by adjusting the design of the MCP chevron pair. A significant improvement in the output pulse peak can be obtained.