Internal mildewed nutmeg is difficult to perceive without cutting the nutmeg open and examining it carefully, which poses a significant risk to public health. At present, macroscopic identification and chromatographic analysis are applied to determine whether nutmeg is moldy or not. However, the former relies on a human panel, with the disadvantages of subjectivity and empirical dependence, whilst the latter is generally time-consuming and requires organic solvents. Therefore, it is urgent to develop a rapid and feasible approach for evaluating the quality and predicting mildew in nutmeg. In this study, the quality and odor characteristics of five groups of nutmeg samples with different degrees of mildew were analyzed by using the responses of an electronic nose combined with chemical profiling. The main physicochemical indicators, such as the levels of α-pinene, β-pinene, elemicin, and dehydro-di-isoeugenol, were determined. The results revealed that the contents of α-pinene, β-pinene, and elemicin changed significantly with the extension of storage time. Through the use of an electronic nose and HS–GC–MS technology to assess the overall odor characteristics of nutmeg samples, it was found that the production of volatile organic compounds (VOCs) such as ammonia/organic amines, carbon monoxide, ethanol, and hydrogen sulfide, as well as changes in the terpene and phenylpropene components of the nutmeg itself, may be the material basis for the changes in odor. The accuracy of the qualitative classification model for the degree of mildew in nutmeg was higher than 90% according to the electronic nose data combined with different machine learning algorithms. Quantitative models were established for predicting the contents of the chemical components, and models based on a BP neural network (BPNN), the support vector machine (SVM), and the random forest algorithm (RF) all showed good performance in predicting the concentrations of these chemical components, except for dehydro-di-isoeugenol. The BPNN performed effectively in predicting the storage time of nutmeg on the basis of the E-nose’s responses, with an RMSE and R2 of 0.268 and 0.996 for the training set, and 0.317 and 0.993 for the testing set, respectively. The results demonstrated that the responses of the electronic nose (E-nose) had a high correlation with the internal quality of nutmeg. This work proposes a quick and non-destructive evaluation method for the quality of nutmeg, which has high accuracy in discriminating between different degrees of mold in nutmeg and is conducive to early detection and warning of moldy phenomena.