Organic membranes are used as temporary substrates for the preparation of Al₂O₃ ion barrier films, and their thickness and compactness significantly affect the electron transmittance and electrical characteristics of the ion barrier microchannel plate (MCP). The micromorphologies of organic membranes with different thicknesses were analyzed using a step tester and metallographic microscope, and the electron transmittance and electrical characteristics of the ion barrier MCP were tested using comprehensive performance test equipment. The results show that the compactness of the organic membrane increases with increasing organic membrane thickness. When the thickness of the organic membrane is as low as 17 nm, the electrons can directly penetrate through the micropores in the organic membrane, which has low compactness; therefore, the MCP with the organic membrane and Al₂O₃ film shows good electron permeability. As the thickness of the organic membrane increases to 136 nm with high compactness, the MCP with the organic membrane and Al₂O₃ film can block almost all incident electrons. This explains why the threshold voltage and loss of current gain of the ion barrier MCP with Al₂O₃ film increase as the thickness of the organic membrane increases. The optimal thickness of the organic membrane is approximately 56–101 nm, as it satisfies the high-current gain and high-compactness ion barrier requirements of MCPs.