The equations of motion for the free vibration of composite thin-walled closed-section beams are derived based on Lagrange’s equation of the second kind. Two stiffness configuration box beams are considered and corresponding closed solutions formula of natural frequency presented. The finite element analysis software, ANSYS is used to calculate the natural frequency and vibration mode shape of composite thin-walled cantilever beams. And the results are compared with closed solutions. The influence of composite elastic coupling and ply angle to thin-walled beams’ free vibration is investigated.