Based on the numerical method proposed in Hu et al. (2018) [22] for Kohn-Sham equation, further improvement on the efficiency is obtained in this paper by i). designing a numerical method with the strategy of separately handling the nonlinear Hartree potential and exchange-correlation potential, and ii). parallelizing the algorithm in an eigenpairwise approach. The feasibility of two approaches is analyzed in detail, and the new algorithm is described completely. Compared with previous results, a significant improvement of numerical efficiency can be observed from plenty of numerical experiments, which make the new method more suitable for the practical problems.