Cinnamon oil has been confirmed as a useful antifungal agent to inhibit Rhizopus nigricans. However, the antifungal mechanism has not been clearly revealed. The possible mechanism as follows were investigated, such as the effects of cinnamon oil on the cell morphology, cell membrane and the activities of the key enzymes in tricarboxylic acid (TCA) cycle. Cinnamon oil can inhibit the mycelia growth of R. nigricans, and scanning electron microscope (SEM) observations revealed that the mycelia morphology alterations of R. nigricans were the markedly shriveled and collapsed hypha, even flatted empty hyphae, swelled cell wall, disrupted plasma membrane, with cytoplasmic matrix leakage. Furthermore, cinnamon oil inhibited the biosynthesis of ergosterol significantly, damaging the cell membrane structure, causing the leakage of intracellular ions, protein and the higher absorbance at 260nm. Moreover, cinnamon oil affected the energy metabolism of R. nigricans by decreasing the activities of succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) in tricarboxylic acid (TCA) cycle.