As a new X-ray imaging system, more and more attention has been paid to the square-hole micro channel plate (MCP) which has the properties of large field of view, high resolution, and collection of enormous radiation to be collimated or focused. However, during the fabrication and process of the MCP, it is hard to avoid generating structural defects in the square holes which greatly influent the imaging quality. The standard square-hole MCP model and MCP models with different structural defects are first set up with the software Tracepro, and then the simulative images of these models are simulated by ray trace method of Monte Carlo. Then the influences of structural defects of Taper type, Twist type and Nonsquare type on imaging quality are analyzed. Based on above simulations, the four samples of MCP are imaged in visible bands with a Nickel-Tungster source. The experimental results are consistent with the simulated images, proving that the simulations are correct. The experimental results show that, all of the three defects can result in area increase and intensity decrease of the central bright spot with expect that the third defect can divide the focused rays into two beams which forms four focus and makes the degradation of energy more serious and thus more seriously influence the imaging quality compared with the other two defects. This paper provides an important basis for the future researches on curved MCP and X-ray optical system based on MCP.