The association between emotion and cognition has recently gathered interest in the field of cognitive neuroscience. However, the neural mechanism of negative emotion processing and its association with cognitive control in early childhood remains unclear. In the present study, we compared the processing of three emotions (i.e., negative, neutral, and positive emotions) and investigated the association between negative emotion processing and cognitive control in children aged 4-6 years (N = 43). Results indicated that children revealed greater brain activation when processing negative emotions than processing neutral and positive emotions. We also found a significant negative association between brain activation during negative emotion processing and reaction times of cognitive control, which represented children with better cognitive control evoked higher brain activation when processing negative emotions. The current study proposes a neural mechanism underlying emotion processing and provides important insights into the risk and future behavioral outcomes of potential psychological disorders.