In this article, according to the thin shell theory of Flugge as well as using a new mathematical procedure, the linear buckling of waffle cylindrical shell under axial load is investigated. Skin and grids are composed of the same isotropic material and the classical boundary conditions of clamped and simply supported are considered. Firstly, using a new mathematical modeling, the structural stiffness matrix of skin and grids is obtained. Then, the equilibrium equations of the shell are derived based on the new stiffness matrix. Finally, these equations are solved using differential quadrature method. The results are compared by the finite element analyses. Comparative results reveal that the present procedure is very stable and accurate. Also, the effects of various geometrical parameters on the linear buckling loads are presented.