Tibetan Plateau is facing serious shortage of forage in winter and spring season due to its special geographical location. Utilization of forages is useful to alleviate the forage shortage in winter and spring season. Consequently, the current study was aimed to evaluate the influence of storage time on the silage quality and microbial community of the maize (Zea mays L.) and faba bean (Vicia faba L.) mixed silage at Qinghai-Tibet Plateau. Maize and faba bean were ensiled with a fresh weight ratio of 7:3, followed by 30, 60, 90, and 120 days of ensiling. The results showed the pH value of mixed silage was below 4.2 at all fermentation days. The LA (lactic acid) content slightly fluctuated with the extension of fermentation time, with 33.76 g/kg DM at 90 days of ensiling. The AA (acetic acid) and NH3-N/TN (ammonium nitrogen/total nitrogen) contents increased with the extension of fermentation time and no significantly different between 90 and 120 days. The CP (crude protein) and WSC (water soluble carbohydrate) contents of mixed silage decreased significantly (P < 0.05) with ensiling time, but the WSC content remained stable at 90 days. The Proteobacteria was the predominant phyla in fresh maize and faba bean, and Pseudomonas and Sphingomonas were the predominant genera. After ensiling, Lactobacillus was the prevalent genus at all ensiling days. The relative abundance of Lactococcus increased rapidly at 90 days of ensiling until 120 days of fermentation. Overall, the storage time significant influenced the silage fermentation quality, nutrient content, and microbial environment, and it remained stable for 90 days of ensiling at Qinghai-Tibet Plateau. Therefore, the recommended storage time of forage is 90 days in Qinghai-Tibet Plateau and other cool areas.