Chinese yam with damaged outer skin can be easily oxidized and infected by spoilage fungi. To find preservatives in the storage of the Chinese yam, Aspergillus niger 103 was isolated, identified, and determined as the dominant spoilage fungus in Chinese yam according to Koch’s postulates. Then, the strain was used as a model to screen antifungal agents and study antifungal mechanisms in this study. We found that cinnamon essential oil was the best antifungal agent, and the minimum concentration against Aspergillus niger 103 was 25 μg/mL. The storage life of Chinese yam could significantly extend by 27.66 days by spraying with cinnamon essential oil (25 μg/mL). To further explore the antifungal mechanism of cinnamon essential oil against Aspergillus niger 103, alkaline phosphatase activity and electrolyte content in the fungal solution were measured. The alkaline phosphatase activity and electrolyte content of the fungal solution with cinnamon essential oil were significantly increased than those without cinnamon essential oil, which showed that the cinnamon essential oil could destroy the integrity of the cell wall and cell membrane of Aspergillus niger 103, and disrupted cellular homeostasis of Aspergillus niger 103.