The improvement of overall uniformity and smoothness of spherical icosahedral grids, the basic framework of atmospheric models, is a key to reducing simulation errors. However, most of the existing grid optimization methods have optimized grid from different aspects and not improved overall uniformity and smoothness of grid at the same time, directly affecting the accuracy and stability of numerical simulation. Although a well-defined grid with more than 12 points cannot be constructed on a sphere, the area uniformity and the interval uniformity of the spherical grid can be traded off to enhance extremely the overall grid uniformity and smoothness. To solve this problem, an overall uniformity and smoothness optimization method of the spherical icosahedral grid is proposed based on the optimal transformation theory. The spherical cell decomposition method has been introduced to iteratively update the grid to minimize the spherical transportation cost, achieving an overall optimization of the spherical icosahedral grid. Experiments on the four optimized grids (the spring dynamics optimized grid, the Heikes and Randall optimized grid, the spherical centroidal Voronoi tessellations optimized grid and XU optimized grid) demonstrate that the grid area uniformity of our method has been raised by 22.60% of SPRG grid, −1.30% of HR grid, 38.30% of SCVT grid and 38.20% of XU grid, and the grid interval uniformity has been improved by 2.50% of SPRG grid, 2.80% of HR grid, 11.10% of SCVT grid and 11.00% of XU grid. Although the grid uniformity of the proposed method is similar with the HR grid, the smoothness of grid deformation has been enhanced by 79.32% of grid area and 24.07% of grid length. To some extent, the proposed method may be viewed as a novel optimization approach of the spherical icosahedral grid which can improve grid overall uniformity and smoothness of grid deformation.