A successful conversion of lignocellulosic biomass into biofuel could be achieved through an ionic liquids (ILs)-pretreatment and an enzyme saccharification. In this study, the fungal strains with high cellulase productions were isolated and identified as Penicillium janthinellum FHH1 and P. oxalicum FLY4. A high cellulase production was obtained at pH 4.0 and 30 °C for P. janthinellum FHH1 with corn stalk and beef extract for 9 days and for P. janthinellum FHH1 with corn stalk and peptone for 7 days. A pH range between 4.0 to 6.0 and a temperature range from 55 °C to 60 °C were applicable for cellulase with high activities during hydrolysis. A high NaCl-stability and a relatively high ILs-stability were found for cellulase obtained from P. oxalicum FLY4. High yields of reducing sugar were obtained by enzymatic hydrolysis of the original corn stalk and ILs-pretreated corn stalk. P. oxalicum FLY4 has a great potential for ILs-assisted fungi in the degradation of lignocellulosic biomass into value-added products.