In a previous paper, we developed a thin polymer film method which was able to measure the real contact area. In this paper, this polymer film method was used to analyze the contact stiffness. In unloading and reloading processes, the real contact area and its distribution were measured by this method at each load. As a result, it turned out the non-uniform contact over the apparent contact area at the low normal load corresponded to rapid change in the contact stiffness. As the normal load was increased, the contact condition gradually approached the uniform contact, leading the contact stiffness to almost constant value. These measurements by the thin polymer film method indicated that the waviness had strongly influenced the contact stiffness more than the surface roughness did. In addition, we carried out the numerical simulation of the contact stiffness on the consideration of only the waviness. The simulated results were in good agreement with the experimental results.