In this study, Candida utilis, Lactobacillus plantarum, and non-starch polysaccharide enzymes (cellulase, laccase, β-glucanase, xylanase, and mannanase) were employed to examine the effects of various microorganism–enzyme combinations on the nutritional composition, fiber structure, and fermentation quality of corn stover and wheat straw. Furthermore, the synergistic effects of these treatments were assessed through the use of in vitro rumen fermentation. The results showed that the microorganism–enzyme combinations significantly increased the crude protein content (p < 0.05), while reducing the acid detergent fiber and neutral detergent fiber levels (p < 0.05) in both substrates. The fermentation broth pH decreased (p = 0.06 for corn stover; p < 0.05 for wheat straw) as a result of the treatments, with a significant increase in the lactate concentration (p < 0.05). The reducing sugar levels varied across the treatments (p < 0.05). Mycotoxin analysis revealed trace amounts of zearalenone, well below the Chinese feed hygiene standard. Scanning electron microscopy showed structural modifications, including fiber breakage and surface wrinkling, in the treated substrates. In vitro rumen fermentation demonstrated significant changes in the NH₃-N production and volatile fatty acid profiles (p < 0.05). In conclusion, the addition of different microorganism–enzyme combinations can effectively improve the nutritional composition, fiber structure, and fermentation quality of corn stover and wheat straw. Among the treatments, the T3 group (25% each of C. utilis, L. plantarum, cellulase, and laccase, with a total addition ratio of 0.3% w/w) exhibited the most pronounced improvement in nutritional value for both corn stover and wheat straw. These findings suggest that microorganism–enzyme combinations effectively enhance the nutritional and fermentative quality of agricultural residues.