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Electroencephalography (EEG) has proven to be effective in emotion analysis. However, current methods struggle with individual variations, complicating the generalization of models trained on data from source subjects to unseen target subjects. To tackle this issue, we propose the Denoising Mixed Mutual Reconstruction (DMMR) model, employing a two-stage pre-training followed by fine-tuning approach. During the pre-training phase, DMMR leverages self-supervised learning through a multi-decoder autoencoder, which encodes and reconstructs features of one subject, aiming to generate features resembling those from other subjects within the same category, thereby encouraging the encoder to learn subject-invariant features. We introduce a hidden-layer mixed data augmentation approach to mitigate the limitations posed by the scarcity of source data, thereby extending the method to a two-stage process. To bolster stability against noise, we incorporate a noise injection method, named “Time Steps Shuffling”, into the input data. During the fine-tuning phase, an emotion classifier is integrated to extract emotion-related features. Experimental accuracy on the SEED and SEED-IV datasets reached 88.27% (±5.62) and 72.70% (±8.01), respectively, demonstrating state-of-the-art and comparable performance, thereby showcasing the superiority of DMMR. The proposed data augmentation and noise injection methods were observed to complementarily enhance accuracy and stability, thus alleviating the aforementioned issues.