Although deep-learning has been successfully applied in a variety of science and engineering problems owing to its strong high-dimensional nonlinear mapping capability, it is of limited use in scientific knowledge discovery. In this work, we propose a deep-learning based framework to discover the macroscopic governing equation of viscous gravity current based on high-resolution microscopic simulation data without the need for prior knowledge of underlying terms. For two typical scenarios with different viscosity ratios, the deep-learning based equations exactly capture the same dominated terms as the theoretically derived equations for describing long-term asymptotic behaviors, which validates the proposed framework. Unknown macroscopic equations are then obtained for describing short-term behaviors, and hidden mechanisms are eventually discovered with deep-learned explainable compensation terms and corresponding coefficients. Consequently, the presented deep-learning framework shows considerable potential for discovering unrevealed intrinsic laws in scientific semantic space from raw experimental or simulation results in data space.