In this work, the surface wrinkle modulation of the film/substrate system caused by eigenstrain in the film is studied. A theoretical model is proposed which shows the change of the wrinkle amplitude is completely determined by four dimensionless parameters, i.e., the eigenstrain in the film, the plane strain modulus ratio between the film and the substrate, the film thickness to wrinkle wavelength ratio, and the initial wrinkle amplitude to wavelength ratio. The surface wrinkle amplitude becomes smaller (even almost flat) for the contraction eigenstrain in the film, while for the expansion eigenstrain it becomes larger. If the expansion eigenstrain exceeds a critical value, secondary wrinkling on top of the existing one is observed for some cases. In general, the deformation diagram of the wrinkled film/substrate system can be divided into three regions, i.e., the change of surface wrinkle amplitude, the irregular wrinkling, and the secondary wrinkling, governed by the four parameters above. Parallel finite element method (FEM) simulations are carried out which have good agreement with the theoretical predictions. The findings may be useful to guide the design and performance of stretchable electronics, cosmetic products, biomedical engineering, soft materials, and devices.