Electroencephalogram (EEG) signals are very weak and have low spatial resolution, which has led to less satisfactory accuracy in cross-subject EEG-based emotion classification studies. Microstate analyses of EEG sources can be performed to determine the important spatiotemporal characteristics of EEG signals. Such analyses can be used to cluster rapidly changing EEG signals into multiple brain prototype topographies, fully utilizing the spatial information contained in the EEG signals and providing a neural representation for emotional dynamics. To better utilize the spatial information of brain signals, source localization analysis on the EEG signals was first conducted. Then, a microstate analysis on the source-reconstructed EEG signals is conducted to extract the microstate features of the data. We conducted source microstate analysis on the participant data from the odor-video physiological signal database (OVPD-II) dataset. The experimental results show that the source microstate feature topologies of different participants under the same emotion exhibited a high degree of correlation, which was proven by the analysis of microstate feature topographic maps and the comparison of two-dimensional feature visualization maps of the differential entropy (DE) and power spectral density (PSD). The microstate features represent more abstract emotional information and are more robust. The extracted microstate features were then used with the style transfer mapping method to transfer the feature data from the source domain to the target domain and were then used in support vector machines (SVMs) and convolutional neural networks (CNNs) for emotion recognition. The experimental results show that the cross-subject classification accuracies of the microstate features in SVMs were 84.90 ± 8.24% and 87.43 ± 7.54%, which were 7.19 and 6.95% higher than those obtained with the PSD and 0.51 and 1.79% higher than those obtained with the DE features. In CNN, the average cross-subject classification accuracies of the microstate features were 86.44 and 91.49%, which were 7.71 and 19.41% higher than those obtained with the PSD and 2.7 and 11.76% higher than those obtained with the DE features.