The metabolic disorder of hepatocytes in non-alcoholic fatty liver disease (NAFLD) leads to the formation of an iron pool which induces the Fenton reaction-derived ferroptosis and the deterioration of liver disease. The elimination of the iron pool for the removal of Fenton reactions is vitally important to prevent the evolution of NAFLD, but quite challenging. In this work, we discover that free heme in the iron pool of NAFLD can catalyze the hydrogenation of H2O2/‧OH to block the heme-based Fenton reaction for the first time, and therefore develop a novel hepatocyte-targeted hydrogen delivery system (MSN-Glu) by modifying magnesium silicide nanosheets (MSN) with N-(3-triethoxysilylpropyl) gluconamide to block the heme-catalyzed vicious circle of liver disease. The developed MSN-Glu nanomedicine exhibits a high hydrogen delivery capacity as well as sustained hydrogen release and hepatocyte-targeting behaviors, and remarkably improves the metabolic function of the liver in a NAFLD mouse model by the relief of oxidative stress and the prevention of ferroptosis in hepatocytes, accelerating the removal of the iron pool in fundamental support of NAFLD prevention. The proposed prevention strategy based on the mechanisms of NAFLD disease and hydrogen medicine will provide an inspiration for inflammation-related disease prevention.