A method is proposed to update the finite element model (FEM) of a tower crane considering the uncertainty of boundary conditions. For tower cranes, the actual dynamic characteristics of the structure are obtained by the vibration testing. First, the FEM of the tower crane considering the uncertainty of boundary conditions is modified. Then, the FEM is updated based on the quadratic response surface method. The non-updated and updated frequencies are compared to the measured frequencies, and the comparison results suggest that the accuracy of the updated results could be improved by considering the influence of boundary conditions. The FEM whose boundary conditions are updated can reproduce modes in the tested frequency range and can predict modes out of the band accurately. These conclusions further show that the method proposed in this paper is feasible and efficient.