Natural product sources recently have been applied to discover drugs for being developed to treat cancer, immunosuppressive disorders, resistant bacteria and viruses. In many instances, the disease targeted natural products serve as tools to unravel the cellular molecular targets and pathways in the disease processes and thus facilitate further development. Here, we identified a natural quinone compound that inhibited human kidney glutaminase activity and the cell growth and proliferation of lung carcinoma A549 and hepatoma HepG2 as well as blocked the anchorage-independent colony formation of HepG2. Autophagy but not apoptosis was found in A549 and HepG2 cells treated with the natural quinone compound. Further investigation demonstrated the natural quinone compound inhibiting glutaminase activity and conceivably depleting the cellular nutrient and energy to induce autophagy for anti-cancer activity.