The effect of metal ions on biological pretreatment was evaluated for improving subsequent enzymatic hydrolysis. Results showed that the efficiency of fungal pretreatment was greatly improved with manganese supplement in biomass. After enzymatic hydrolysis of 28-d pretreated corn stover, maximum glucose yield was 308.98mg/g corn stover with manganese supplement, which increased by 61.39% as compared to the conventional fungal pretreatment. Furthermore, manganese also enhanced the production of ethanol, corresponding to a high ethanol conversion (83.39%). Manganese greatly improved the delignification of Irpex lacteus specially. Correspondingly, the efficiency of saccharification and fermentation was closely related to the removal of lignin. This study showed a promising effect of manganese on fungal pretreatment and the production of biofuels.