Purpose <p>Empathy has become a key area of research in children with autism spectrum disorder (ASD) in recent years. However, the neural characteristics of empathy in children with ASD remain controversial. To advance the understanding of the neural mechanism of ASD’s empathy and test the classic empathy imbalance hypothesis, it is necessary to explore the cognitive-affective empathy in young children with ASD from another electrophysiological perspective in detail.</p> Methods <p>The present study explored the specific neural characteristics of children with ASD and typically developing children under cognitive empathy and affective empathy via simultaneous EEG recording of social animation, which would be able to capture reliable and effective evidence in children with ASD.</p> Results <p>The present study mainly revealed that the ASD group had abnormal electrophysiological characteristics under cognitive empathy, including increased functional connectivity in the θ band and abnormalities in the microstate classes C and D. Incidentally, this study also roughly found that the severity of autism symptoms was significantly correlated with the β-band amplitude of certain brain regions when viewing cognitive empathy clips, whereas the severity of autism symptoms was significantly correlated with the θ-band amplitude when viewing affective empathy clips.</p> Conclusion <p>The present study supported the empathy imbalance hypothesis in young children with ASD and might indicate that children with ASD have distinct neural characteristics related to cognitive empathy and affective empathy processing. Future studies can combine eye movement measurements while watching animations, and further longitudinal studies on the electrophysiological characteristics of empathy in children with ASD.</p>