The cleft lip and palate (CLP) is one of the most common craniofacial malformations in humans. We collected functional magnetic resonance data of 23 CLP patients before rehabilitation training (Bclp) and 23 CLP patients after rehabilitation training (Aclp), who were performing Chinese character pronunciation tasks, and performed brain activation analysis to explore the changes of brain mechanism in CLP patients after articulation disorder rehabilitation training. The study found that Aclp group had significant activation in the motor cortex, Broca area, Wernicke area and cerebellum. While the Bclp group had weak activation in the motor cortex with a small activation range. By comparing the differences and co-activated brain regions between the two groups, we found that rehabilitation training increased the activity level of negatively activated brain areas (cerebellum, left motor area, Wernicke area, etc.) to a positive level. At the same time, the activity level of weakly activated brain areas (right motor area, Broca area, etc.) was also increased. Rehabilitation training promoted the activity level of articulation-related brain regions. So that the activation intensity of articulation-related brain regions can be used as a quantifiable objective evaluation index to evaluate the effect of rehabilitation training, which is of great significance for the formulation of rehabilitation training programs.