Jerusalem artichoke residue (JR) was co-ensiled with grain stillage (GS) at various weight mixing ratios (JR only, 4 to 1, 2 to 1, 1.2 to 1, 1 to 1.5, 1 to 2.7, 1 to 7, and GS only) for 10, 30, and 60 d for agricultural biomass storage. Results showed that the middle level of GS to JR ratios, e.g., 1.2 to 1 and 1 to 1.5, achieved the best co-ensiling performance among all studied ratios. The water-soluble carbohydrate (WSC) contents were significantly higher than those of the other treatments (p < 0.05), and the lignocellulose contents were significantly lower than those of other treatments (p < 0.05). The silages ensiled at the above-mentioned ratios had a higher feed value and biodegradation potential than other ratios. Lactobacillus was the dominant bacterial species during the ensiling process, and its relative abundance was significantly correlated with the content of different components, e.g., WSC, crude protein, and starch, as well as fermentation characteristics. Fungal species, e.g., Kluyveromyces and Monascus were also observed, and the relative abundance of which was positively correlated with different nutritional components. In conclusion, GS and JR can be successfully stored via co-ensiling.