Reducing aerobic spoilage and rumen greenhouse gas emissions from anaerobically fermented feeds remains critical challenges in energy saving and environmental protection of animal husbandry. This study investigated the effects of dandelions, both alone and combined with Lactobacillus plantarum and Lactobacillus buchneri (LAB) on fermentation quality, bacteriome and mycobiome after 180 d of anaerobic and 4 d of aerobic fermentation of whole-plant corn. In vitro dry matter digestion (IVDMD) and gas production from anaerobically fermented whole-plant corn were also assessed. The results demonstrated that dandelions, either alone or combined with LAB, effectively improved fermentation quality by reducing NH3-N concentrations (22.72–25.99%) after anaerobic fermentation, decreasing the proliferation of yeast and molds to enhance the aerobic stability. Notably, the changes in the bacteriome were more pronounced than those in the mycobiome after aerobic exposure. The addition of dandelions or the combination reduced Acetobacter fabarum abundance, a member of the Acetobacter that was spoilage-induced microbe indicated by correlation analysis. Besides, these treatments facilitated competition relations of microbiome which contributed to the enhanced aerobic stability. Furthermore, dandelions reduced CH₄ and CO₂ emissions by 14.88 and 13.73%, respectively, and also positively influencing IVDMD by 4.46%. Collectively, dandelion alone or combined with LAB are promising strategies to improve the aerobic stability of anaerobically fermented whole-plant corn, a process linked to the interactions between the bacteriome and mycobiome, and to contribute to clean production by reducing rumen CH₄ and CO₂ emissions.