Nano-bubble water (NBW) was applied to anaerobic digestion (AD) to alleviate volatile fatty acids (VFAs) inhibition, improve the buffering capacity and CH4 production in this work. Results indicated that NBW accelerated the consumption of VFAs and prevented inhibition due to VFAs accumulation. Additionally, NBW facilitated a rapid increase in partial alkalinity (PA) and total alkalinity (TA) as well as a corresponding rapid decrease in intermediate alkalinity (IA)/PA and VFA/TA, thereby improving buffering capacity and alleviating VFAs inhibition. Moreover, CH4 production improved by more than 12.2% by NBW. Similarly, the activities of the extracellular hydrolases and coenzyme F420 increased. Besides, NBW increased the abundance of microbial community and strengthened the metabolic pathways of hydrogenotrophic methanogens, which could be the intrinsic mechanism by which NBW alleviated VFAs inhibition, improved system stability, and increased CH4 production. This study demonstrates that NBW supplementation can be an effective method for mitigating frequent VFAs inhibition.