The multidimensional positive definite advection transport algorithm (MPDATA) is an important numerical method for the computation of atmospheric dynamics. MPDATA is second-order accurate, positive definite, conservative, and computationally efficient. However, the method is problematic in which it results in a loss of precision when computing a nonuniform irregular grid. Furthermore, research revealed two reasons for this problem. On the one hand, numerical discretization of boundary derivatives of the finite-volume method is incompatible with nonuniform meshes (or grids); on the other hand, the up-wind scheme of staggered grids is not applicable to the calculation of irregular grids. We overcome these two problems by using the multipoint Taylor expansion method to obtain a boundary derivative numerical approximation scheme that does not depend on the grid structure. Furthermore, combined with the well-balance central-upwind scheme, a positive definite advection scheme for irregular meshes is proposed. Then, the positivity of the new numerical scheme is analyzed. Finally, the result of this study is verified by numerical simulation.