The traditional deterministic finite element updating only deals with a single specified structure. However, it is conceivable that uncertainties such as the geometric tolerances and physical properties of the material, will lead to the variability of the structural behaviors for a panel of nominally identical structures. In this case, we have to resort to the stochastic finite element updating approach to handle the problem. Based on the stochastic perturbation method, a new framework of stochastic finite element updating using data from modal test is proposed in this paper. The efficiency of updating is improved through dividing the updating procedure into two independent parts: the deterministic part updating and the stochastic part updating. The Bayesian statistical method is employed to improve the estimation accuracy of stochastic part updating. Two numerical examples are used to demonstrate the effectiveness and the efficiency of the proposed method.