The objective of this study was to explore excellent silage production through co-ensiling whole-plant cassava and corn stalk, and different ratios of whole-plant cassava (0%, 10%, 20%, 30%, 40%, and 50%, fresh-matter basis) co-ensiled with corn stalk were analyzed based on the silage bacterial community, function profile, and microbial ecological network features. The results demonstrated that co-ensiling 30% whole-plant cassava with 70% corn stalk could be considered an efficient mode of production. The mixed silage showed great quality, as reflected by the reduced pH value and concentrations of acetic acid, butyric acid, and ammonia nitrogen and the enhanced lactic acid concentration, V-score, and nutritional value compared with corn stalk ensiled alone. Meanwhile, co-ensiling restricted the undesirable bacterial Acetobacter fabarum of corn stalk and Pseudomonas aeruginosa of whole-plant cassava and raised the abundance of lactic acid bacteria (LAB) such as Levilactobacillus brevis, Lactiplantibacillus plantarum, Lactobacillus harbinensis, etc. Besides that, the predicted functions of the bacterial community showed large differences in mixed silage compared with whole-plant cassava or corn stalk ensiled alone. Moreover, the analysis of co-occurrence networks showed that mixed silage affected microbial network features, module numbers, and bacterial relative abundances and weakened the complexity and stability of the networks compared with whole-plant cassava single silage. Furthermore, silage microbial community composition had a huge impact on the network properties, and undesirable Pseudomonas aeruginosa played a crucial role in the complexity and stability. Overall, this study revealed the characteristics of whole-plant cassava with corn stalk mixed-silage microbial communities and co-occurrence network modules, complexity, and stability and partly clarified the microbial mechanism of co-ensiling for producing high-quality silage. The findings of this study have important implications for deeply understanding the ensiling process and precisely regulating silage fermentation quality.