Suppression of the secondary electron (SE) multipactor is a key issue for improving the performance of high power microwave devices and particle accelerators. The decrease of the SE emission yield (SEY) by using certain surface morphology is one of the effective methods. To optimize the surface morphology, we simulate the SE emissions of different surface structures by using the Monte Carlo method. The effects of geometric parameters, such as duty ratio of area, depth-to-height ratio, pattern and its arrangement on SEY are investigated. For surface morphology with patterns of square, round and triangle, and for both convex and concave structures, the corresponding values of SEY first decrease and then become steady with the increase of duty ratio of area and depth-to-height ratio. For convex structures, the values of SEY are different for different pattern shapes, in which triangle pattern has the smallest SEY. However, the value of SEY is nearly independent of arrangement of pattern. For concave structures, on the other hand, the value of SEY is scarcely different for different patterns or different arrangements. In general, a convex structure has a better suppression effect than a concave structure if other geometric parameters are identical. The shading effect from side wall of structure is found to be the intrinsic reason of the suppression effect.