This study aimed to investigate the effects of microbial inoculants (L) and molasses (M) on the bacterial and fungal microbiomes of barley silage after the aerobic stage. The addition of molasses and microbial inoculants improved the aerobic stability of barley silage. The ML silage, which had a low pH value and high lactic and acetic acid contents, remained aerobically stable for more than 216 h. The ML silage exhibited low bacterial and high fungal diversities. Microbial inoculants and molasses enriched the abundance of Lactobacillus in silage after aerobic exposure. The enrichment of L. buchneri was significant in ML silage at days 5 and 7 during the aerobic stage. The abundance of harmful microorganisms, such as aerobic bacterial including Acinetobacter, Providencia, Bacillus, and yeasts including Issatchenkia, Candida, and Kazachstania, were suppressed in ML silage. M and L had an impact on bacterial and fungal microbes, resulting in the improvement of fermentation quality and reduction of aerobic spoilage in barley silage.