Fungal spoilage of food and the excessive use of chemical disinfectants serves potential adverse effects on human health and the environment. Consequently, there is a growing interest in exploring natural alternatives, particularly plant-derived antimicrobial preservatives. Cinnamon extracts are known for their antifungal activity, but most research has focused on essential oils, rarely on other bioactive components. This study assessed the antifungal activity and underlying mechanisms of four components—trans-cinnamaldehyde, cis-2-methoxycinnamic acid, coumarin, and o-methoxycinnamaldehyde—extracted from Cinnamomum cassia Presl (cinnamon) against Aspergillus flavus and Penicillium citrinum. These cinnamon components can inhibit the two fungi strains at the minimum inhibitory concentration ranged from 0.30 to 8.55 mmol/L. These components can disrupt fungal cell membranes by enhancing relative electrical conductivity and cytoplasmic content leakage, reducing ergosterol content, and increasing malondialdehyde level. Additionally, they can affect fungal cell wall integrity, leading to the leakage of alkaline phosphatase and alterations in the contents of β-1,3-glucan and chitin. Moreover, the cinnamon components influenced the activities of malate dehydrogenase, succinate dehydrogenase, as well as adenosine triphosphate levels. The observed suppression of fungal contamination in A. flavus and P. citrinum suggests that these cinnamon components as potential natural antifungal agents.