The jujube is one of the most popular fruits in China because of its delicious taste and high nutritional value. It has a long history of usage as an important food or traditional medicine. However, the jujube is easily infected by fungi, which causes economic losses and threatens human health. When the jujube was infected by Aspergillus niger (H1), the changes in nutritional qualities were determined, such as the content of total acid, vitamin C, reducing sugar, etc. In addition, the ability of A. niger (H1) to produce ochratoxin A (OTA) in different inoculation times and culture media was evaluated, and the content of OTA in jujubes was also analyzed. After jujubes were infected by A. niger (H1), the total acid, and vitamin C contents increased, while the total phenol content decreased, and the reducing sugar content increased after an initial decrease. Although A. niger (H1) infection caused the jujubes to rot and affected its quality, OTA had not been detected. This research provides a theoretical foundation for maximizing edible safety and evaluating the losses caused by fungal disease in jujubes.