Microchannel plates (MCPs) are widely utilized as key device components in various photomultipliers; however, the performance of MCPs cannot be further improved by traditional processing. Atomic layer deposition (ALD) is a promising route to prepare a composite conductive layer and secondary electron emission (SEE) layer structure on the inner wall of the MCP. Moreover, ZnO is an essential component of a composite conductive layer, which is located at the bottom of the SEE layer and significantly influences the SEE coefficient, which, in turn, affects the gain performance of MCPs. Herein, ALD is used to deposit different thicknesses of ZnO films (1-50nm) on an Si substrate, resulting in an ZnO/Si double-layer film structure. The relationship between the SEE coefficient and the primary electron energy of ZnO films with different thicknesses was established. The maximum secondary electron yield value of 2.04 is achieved at a film thickness of 30nm. Moreover, Dionne's SEE model and theory of semiconductors are used to simulate and verify the experimental results. These results provide useful guidelines for the development of ALD-MCPs.