In this work, finite element analysis on the surface instability process of a film-substrate system with the sinusoidal surface structures is systematically carried out by using ABAQUS finite element software. The effects of the elements on surface instability morphology, including ratio of amplitude to wavelength of the sinusoidal structure, the modulus ratio of film to substrate, the film thickness and the pre-stretched deformation, are discussed. The results show that the modulus ratio and the film thickness have considerable influence on the wavelength of the film surface instability. The ratio of amplitude to wavelength of the sinusoidal structure plays a significant role in differentiating the instability wavelength at the peak and trough of the sinusoidal structure. Means to control the instability morphology of the film-substrate systems by various combinations of the above parameters are proposed. Compared with the experimental results, the reliability of the numerical simulation method is qualitatively verified. The research work is of reference value for exploring the instability of thin films with complex surface structures.