Cinnamaldehyde (CA) is a natural and safe agent with prominent antimicrobial activities. Its use in liquid phase has been reported in-depth, but few studies have elucidated the application and the antimicrobial mechanism of CA in vapor phase. This work evaluated the antifungal effects of CA vapor against Aspergillus niger HY2 and its effectiveness in paddy matrices was also explored. The results showed that CA in vapor phase was more effective than CA in liquid phase. CA vapor could inhibit the ergosterol synthesis of A. niger HY2, promote malondialdehyde production and cause plasma membrane damage, which would further lead to the leakage of intracellular contents. The decrease of mitochondrial membrane potential, adenosine triphosphatase, and succinate dehydrogenase activities also revealed that mitochondrial function was impaired. The accelerated storage test showed that CA vapor could inhibit the increase of fatty acid content, and then delay the deterioration of paddy quality. But the effect of CA on inhibiting the growth of A. niger HY2 on paddy was minor. In summary, all results above confirmed that the antifungal activity of CA vapor was mainly conducted by disrupting mycelial ultrastructure. Therefore, CA vapor can be used as a promising antifungal agent in food storage and transportation.