To improve the performance of microchannel plate (MCP) such as gain and lifetime, in this paper, Al2O3/MgO composite layer materials are deposited by Atomic Layer Deposition (ALD) technique in MCP. The composite layer deposited in the channel wall with large aspect ratio (40:1) can increase the second electron emission coefficient of the channel wall. Magnesium oxide has a high secondary electron yield and has good application prospect in photoelectric detection devices. However, magnesium oxide is easy to deliquesce in air and has poor stability, which is an urgent problem to be solved. In this paper, ALD-MCP with Al2O3/MgO/Al2O3 composite layer was proposed so that MgO layer can be protected by Al2O3 layer. The thickness nonuniformity of MgO film in the channel with large aspect ratio can reach 3.8% by optimizing the deposition process. The effects of film thickness and deposition temperature on the gain of MCP and the operating voltage of MCP-PMT (gain@107) were studied to obtain the best film fabrication process. The ALD-MCP with Al2O3/MgO/Al2O3 composite layer can be stable storage for 14 days in the nitrogen cabinet by the surface protection of 20 cycles Al2O3. The optimum film deposition process of MgO:deposition temperature is 210 ℃, thickness of 50 cycles (6.1 nm). The gain (@550 V) of the ALD-MCP with Al2O3/MgO/Al2O3 (5/50/20) composite layer deposited by ALD can be increased by 3.9 times. When the ALD-MCP coated with Al2O3/MgO/Al2O3 composite layer is used in MCP-PMT, the performance of MCP-PMT improved significantly, including the operating voltage, the peak-valley ratio, pulse height resolution and lifetime. The operating voltage decrease from 1880 V to 1740 V and the output charge can reach 10 C/cm2. Applied Al2O3/MgO composite layer in MCP can effectively improve the gain, reduce the operating voltage of the device and extend the lifetime. The use of Al2O3 film layer for encapsulation protection is very important for the application of MgO materials in MCP and other photoelectric detection components. At the same time, the deposition of MgO matrix composite layer in MCP can also expand the application of MCP in detecting active ions.