Time is an important element for cognitive processes. Timing and time perception have been investigated by neuroscientists and psychologists for many years. It is well accepted that emotions could alter our experience of time. Previous studies of the emotional modulation on temporal perception focus primarily on behavioral and psychological experiments. In recent years, studies about the neurophysiological mechanisms of time perception have made some progress. Therefore, researchers started to explore how emotions influence our sense of time on the aspects of neural networks, neurotransmitters and synaptic plasticity. In this paper, we tried to review current studies about the effects of emotional regulation on time perception and the relevant neurophysiological mechanisms. This review will help us to deeply understand the neural mechanisms of time perception.