In Radovitzky and Ortiz (Comput Methods Appl Mech Eng 172(1–4):203–240, 1999), an error estimation technique for nonlinear PDEs is presented to adaptively generating mesh, based on the reduction of the order of the approximate polynomial. In this paper, following a similar analysis framework, we propose an a posteriori error estimation for Kohn–Sham equation by coarsening mesh. An upper bound for the difference of the total energies on two successively refined meshes is derived by the numerical solutions on two meshes through an asymptotic analysis, which finally generates an a posteriori error estimation. A variety of numerical tests show that such an a posteriori error estimation works very well in our h-adaptive finite element method framework. In addition, to further improve the efficiency, we solve a Poisson equation instead of the Kohn–Sham equation on the coarsened mesh. The effectiveness of this improvement is analyzed and numerically examined.