An approach of parameter identification for predicting uncertainties in honeycomb sandwich composite is conducted in this paper. The initial finite element model of honeycomb plate is constructed by application of an appropriate sandwich theory, in which the equivalent parameters are predicted by homogenization method. According to analysis of the internal honeycomb structure and the relative sensitivity of eigenvalues respect to system parameters, the sensitive parameters which also contain uncertainties (Gcxz, Gcyz and thickness of the face sheet) are selected to be identified. Through modal experiments of six different honeycomb plates with free-free boundary condition, the mean value and deviation of the modal frequencies are obtained, using which the uncertain parameter identification of honeycomb sandwich plate is conducted. Results show that when considering the uncertainty in honeycomb sandwich composite, the proposed identification method can be used for accurately identifying the mean value and deviation of the uncertain parameters, the dynamical finite element model with statistical significance can be constructed at the same time.