The polysaccharide chitosan possesses broad-spectrum antimicrobial properties and has proven effective in controlling various postharvest diseases in fruits. Nevertheless, the fundamental mechanisms underlying its action remain unclear. In this study, the antifungal effects of chitosan with different molecular weights against Fusarium avenaceum, a pathogen causing root rot in Angelica sinensis, were evaluated. Additionally, the potential mechanisms of these effects were explored at the microstructural and transcriptomic levels. Notably, low-molecular-weight chitosan (20 kDa) exhibited superior antifungal activity when compared to high-molecular-weight chitosan (500 kDa and 1000 kDa). The half-maximal inhibitory concentration (IC