To ameliorate the disadvantages of imaging system coupled with imaging fiber bundle, a method by adding square aperture microlens arrays at both entrance and exit ends of the imaging fiber bundle is proposed to increase the system’s coupling efficiency. The expressions for solving the parameters of both ends’ microlens units are deducted particularly. The microlens arrays used for an infrared imaging fiber bundle with the single fiber diameter of 100 μm and core diameter of 70 μm are designed by this method. The simulation results show that compared with the system without microlens arrays, the fill factor of the imaging fiber bundle coupled microlens arrays system is increased from 44.4% to more than 90%, and the coupling efficiency is doubled too. So the design method is correct, and the introduction of microlens arrays into imaging fiber bundle coupled system is feasible and superior.