Filamentous fungi such as Aspergillus spp., Trichoderma spp., and Penicillium spp. are frequently used to produce high concentrations of lignocellulosic enzymes. This study examined the discrepancies in the compositions and dynamic changes in the extracellular enzyme systems secreted by Aspergillus niger ATCC1015, Trichoderma reesei QM9414, and Penicillium oxalicum 114-2 cultured on corn stover and wheat bran. The results revealed different types and an abundance of monosaccharides and oligosaccharides were released during incubation, which induced the secretion of diverse glycoside hydrolases. Both the enzyme activities and isozyme numbers of the three fungal strains increased with time. A total of 279, 161, and 183 secretory proteins were detected in A. niger, T. reesei, and P. oxalicum secretomes, respectively. In the A. niger secretomes, more enzymes involved in the degradation of (galacto)mannan, xyloglucan, and the backbone of pectin distributed mostly in dicots were detected. In comparison, although P. oxalicum 114-2 hardly secreted any xyloglucanases, the diversities of enzymes involved in the degradation of xylan and beta-(1,3;1,4)-d-glucan commonly found in monocots were higher. The cellulase system of P. oxalicum 114-2 was more balanced. The degradation preference provided a new perspective regarding the recomposition of lignocellulosic enzymes based on substrate types.