In this paper, a new method of using the electric field numerical weight to process the inhomogeneous cells is proposed, which is to resolve the problems such as high errors and parallel direction excluded in the existing finite-difference time-domain method. Instead of deriving average dielectric constant, the new method weights the electric field strength, which is the true solving variables, according to the mean value theorem, and then the length of the integral path is multiplied by the weight. In the new method both the discontinuous effects of inhomogeneous Ampere cell and the ones of inhomogeneous Faraday cell are taken into account, so it is accurate, easy to implement, versatile, and applicable to any of the various positional relationships between the dielectric interface and the electric field strength variable. A numerical model of dielectric filled circular waveguide is used for the numerical calculation and simulation, in which the deviations of the characteristic roots in two-dimensional TE mode solved by different methods from the theoretical ones are compared, and the anisotropies of different methods are also compared. The numerical result shows that the characteristic roots solved by the presented method are closer to the theoretical ones and the anisotropy caused by the proposing method is lower, which proves that this method is more efficient to process the inhomogeneous cells.