In this paper, a gradient flow model is proposed for conducting ground state calculations in Wigner formalism of many-body system in the framework of density functional theory. More specifically, an energy functional for the ground state in Wigner formalism is proposed to provide a new perspective for ground state calculations of the Wigner function. Employing density functional theory, a gradient flow model is designed based on the energy functional to obtain the ground state Wigner function representing the whole many-body system. Subsequently, an efficient algorithm is developed using the operator splitting method and the Fourier spectral collocation method, whose numerical complexity of single iteration is $O(n_{\rm DoF}\log n_{\rm DoF})$. Numerical experiments demonstrate the anticipated accuracy, encompassing the one-dimensional system with up to $2^{21}$ particles and the three-dimensional system with defect, showcasing the potential of our approach to large-scale simulations and computations of systems with defect.

20 pages, 6 figures