A high stiffness waterproof roof panel pad for a vehicle, which is configured by stacking and laminating a waterproof reinforcing layer coated with PE layers on both surfaces of a urethane foam pad, thereby reinforcing the stiffness of a vehicle body panel, preventing the pad from becoming wet due to dew condensation and thus increasing noise and vibration reduction effects and having a waterproof function. Additionally, a method of manufacturing the waterproof roof panel pad includes preparing a hard urethane foam pad, preparing a waterproof reinforcing layer of which both surfaces are coated with PE layers, stacking the waterproof reinforcing layer on both surfaces of the urethane foam pad, laminating the PE layer in contact with the urethane foam pad and integrally forming the urethane foam pad and the waterproof reinforcing layer, and performing a cutting operation according to a shape and a size of a roof panel.