Aiming at the problem that the samples' (indexes') sequence influences the incidence order in the grey incidence model for the current panel data, a new grey incidence model under the panel data is established. Considering the dynamic development characteristics of the multivariate panel data, the corresponding changing incremental and changing speed are added according to different indexes in the matrix characterization. Then the grey incidence model is proposed based on the root mean square distance(RMSD) that is used to measure the similarity of the index matrix, and its specification and isotonicity are also be discussed. A numerical example illustrates that the incidence degree is not influenced by the sequence of multivariate sample. Finally, the proposed model is applied into the recognition of the risk factors of drought vulnerability. The correlation between the regional agricultural drought vulnerability and its influence factors is clarified, which provides theoretical support for regional agricultural drought risk management.