Fiber metal laminates (FMLs) are hybrid materials consisting of metals and fiber-reinforced composite materials. The characteristics of interfaces between metal layers and layers of composites directly determine the damage tolerance and impact resistance of FMLs. In this study, the effects of surface pre-treatment and adhesive quantity on the interface of FMLs were investigated. Aluminum substrates were treated with sandpaper and anodizing. The treated surface structure and joint shear strength were evaluated to analyze the bonding interface quality. The results show that the surface roughness, structure and thickness of the anodized films affect the interface characteristics and adhesion strength. A porous oxide layer was formed on the substrate surface after anodization, resulting in a better wetting surface than that of sanded. Moreover, statistical analysis of the surface structures reveals that the shear strength of phosphoric acid anodizing treatment was higher than other anodizing. With the increase in adhesive layers, the lap shear strength was markedly improved at the beginning but slowly increased thereafter. From the results, the surface pre-treatment and adhesive quantity could be optimized to improve the manufacturing process of FMLs.