Ruppeiner geometry has been found to be a novel promising approach to uncover the microstructure of fluid systems and black holes. In this work, combining with the micro model of the Van der Waals fluid, we shall propose a first microscopic interpretation for the empirical observation of Ruppeiner geometry. Then employing the microscopic interpretation, we disclose the potential microstructure for the anti-de Sitter black hole systems. Of particular interest, we obtain the microscopic interaction potentials for the underlying black hole molecules. This significantly strengthens the study towards to the black hole nature from the viewpoint of the thermodynamics.