The obvious deformation of the box girder being due to some cross-section distortion effect,affects seriously the normal use of the bridge. Based on the Hamiltonian dual calculating system and the precise integration method,the Hamilton canonical equation about free vibration analysis of thin-walled box girder considering distortion was established by suing the basic assumption of the generalized coordinate method,and the corresponding programs were compiled by MATLAB. The dichotomy was used to calculate natural frequencies of structures. Finally,the comparative analysis of specific examples proved the correctness and feasibility of this approach.