Here we present a robust physiological model for the recognition of human emotions, called Deep Physiological Affect Network. This model is based on a convolutional long short-term memory (ConvLSTM) network and a new temporal margin-based loss function. Formulating the emotion recognition problem as a spectral-temporal sequence classification problem of bipolar EEG signals underlying brain lateralization and photoplethysmogram signals, the proposed model improves the performance of emotion recognition. Specifically, the new loss function allows the model to be more confident as it observes more of specific feelings while training ConvLSTM models. The function is designed to result in penalties for the violation of such confidence. Our experiments on a public dataset show that our deep physiological learning technology significantly increases the recognition rate of state-of-the-art techniques by 15.96% increase in accuracy. An extensive analysis of the relationship between participants’ emotion ratings and physiological changes in brain lateralization function during the experiment is also presented.