Based on the existing vector finite element method (VFEM) and the recently developed interval filed model, an interval vector finite element method (IVFEM) is proposed in this paper to deal with the eigenvalue problems of the dielectric-filled waveguide with material uncertainties. The uncertain dielectric material properties are modeled by interval fields due to the limited information and the spatially related variations. The interval field is firstly approximated by a finite number of interval variables by the interval Karhunen-Loeve (K-L) expansion, and then the IVFEM is formulated by incorporating the interval uncertainties into the eigenvalue equations of the VFEM for the dielectric-filled waveguide. The perturbation method is employed to calculate the upper and lower bounds of the eigenvalues that can be used to estimate the transmission properties of the waveguide. Three numerical examples are investigated to demonstrate the validity of the presented method.