Aflatoxins in moldy peanuts are seriously toxic to humans. These kernels need to be screened in the production process. Hyperspectral imaging techniques can be used to identify moldy peanuts. However, the changes in spectral information and texture information caused by the difference in moisture content in peanuts will affect the identification accuracy. To reduce and eliminate the influence of this factor, a data augmentation method based on interpolation was proposed to improve the generalization ability and robustness of the model. Firstly, the near-infrared hyperspectral images of 5 varieties, 4 classes, and 3 moisture content gradients with 39,119 kernels were collected. Then, the data augmentation method called the difference of spectral mean (DSM) was constructed. K-nearest neighbors (KNN), support vector machines (SVM), and MobileViT-xs models were used to verify the effectiveness of the data augmentation method on data with two gradients and three gradients. The experimental results show that the data augmentation can effectively reduce the influence of the difference in moisture content on the model identification accuracy. The DSM method has the highest accuracy improvement in 5 varieties of peanut datasets. In particular, the accuracy of KNN, SVM, and MobileViT-xs using the data of two gradients was improved by 3.55%, 4.42%, and 5.9%, respectively. Furthermore, this study provides a new method for improving the identification accuracy of moldy peanuts and also provides a reference basis for the screening of related foods such as corn, orange, and mango.