Shear fatigue damage to the waterproof cohesive layer has not received enough attention in bridge deck pavement design. Meanwhile, there is less theoretical basis for the design of a waterproof cohesive layer. In this study, direct shear and shear fatigue tests were used to compare the shear strength and fatigue performance of waterproof adhesive materials under different disposal schemes for a cement slab surface, bonding materials, and spreading schemes, and the recommended optimal dosage of waterproof adhesive material for the bridge deck is given. Based on the shear fatigue tests results of indoor waterproof adhesive materials, an equation for prediction fatigue at 15 °C was established and temperature correction was applied. Based on these results, we propose a waterproof cohesive layer design method for bridge deck pavement with interlayer shear damage as the design index. The life expectancy of the shear damage between the decks was calculated for a real bridge deck. These results provide scientific guidance for design of a waterproof cohesive layer in a bridge deck, which can effectively extend the service life of a bridge deck.