A small amount of micro-pores are formed on the substrate surface of some materials after laser cladding, and the existence of the micro-pores directly results in the mechanical properties of the material during the laser shock peening. The numerical simulation of micro-pores integrated laser shock peening of aluminum alloys was carried out. The two-dimensional axisymmetric finite element models of homogeneous substrate and micro-pore substrate were established in ABAQUS finite element software. The effects of micro-pores in the cladding layer on the velocity, the residual stress field, the plastic deformation and the energy change of the shock wave during laser shock processing were researched. The basic mechanisms of these effects have been systematically studied. The numerical simulation results show that there is significant compressive stress around the micropores compared with the homogeneous substrate. The existence of micro-pores weakens the propagation velocity of the shock wave, and the wave velocity decreases by about 3.94%. In addition, the existence of the micro-pores affects the final energy absorption.