EEG-based hyper-scanning refers to two or more subjects engaged in a task together or performing the same action together while neurophysiological signals are simultaneously recorded from them. This is one of the manners for investigating between-subject neural activities involved in social interactions. Emotion perception plays an important role in human social interactions. Interaction and emotional state influence each other. In this study, we aim to investigate how between-subject interaction modulates emotion perception based on event related potentials (ERPs), connectivity analysis and classification analysis. We found that there are distinct differences appearing between paired subjects who performed the task together, which are early ERP components (N250 and N400), late ERP components (P1500 and N1500), and the greater amplitude in N250 for the seconding responding subject compared to the first one. In the exploration of connectivity using phase locking value (PLV), we found that there are significant differences among different frequency bands for each subject under positive and negative stimuli and the significant difference of hyper-connectivity existed in the gamma frequency band between positive and negative stimulus trials. In the classification analysis, we compared the hyper-features for two individual subjects separately, the performance was improved when hyper-features of the PLV was employed compared to the features of power spectrum density.