The minimum cost control problem is one of the most important issues in controlling complex networks. Different from the previous works, in this paper, we consider the minimum cost control problem with selectable inputs by adopting the cost function summed over both quadratic terms of system input and system state with a weighting factor. To address such an issue, the orthonormal-constraint-based projected gradient method is proposed to determine the input matrix iteratively. Convergence of the proposed algorithm is established. Extensive simulation results are carried out to show the effectiveness of the proposed algorithm. We also investigate what kinds of nodes are most important for minimizing average control cost in directed stems/circles and small networks through simulation studies. The presented results in this paper bring meaningful physical insights in controlling the directed networks from an energy point of view.