Functional composite skin has been increasingly used in advanced flight vehicles and some industrial complex systems. For example, it is usually used as aerodynamic sealing structure of the gap between main wing surface and movable control surface so as to ensure the continuity of the wing surface, which can effectively improve flight performance and stealth performance of flight vehicles. The dynamic characteristics analysis of functional skin is of great significance for its reliability and stability design. In this study, the dynamic characteristics of functional composite skin under different installation and flight states, including the original state (non-contact state), the installation state (considering nonlinear contact boundaries), and the working state (considering both nonlinear contact boundary and pressured inner surface), are analyzed based on FEM numerical simulations. The results indicate that: unlike the two-dimensional uniform plates, new “bending-torsion-coupling” modal shape appears in the composite laminates. The modal frequencies and modal shapes of functional skin can be mainly divided into two kinds, i.e. the contact-modes and non-contact-modes, while various non-linear contact conditions are considered, which provides a guide to further dynamic, and particularly aeroelastic, analysis of such structures during structural configuration design and strength assessment. And, their modal behaviors in terms of chordwise and spanwise characteristics are significantly different. Moreover, the contact states and modal shapes are affected by flight velocity, and, even in some states, the dynamic characteristics will undergo substantial changes principally because of the different contact states.