Introduction Cleft lip and/or palate (CLP) patients still have severe speech disorder requiring speech rehabilitation after surgical repair. The clarity of language rehabilitation is evaluated clinically by the Language Rehabilitation Scale. However, the pattern and underlying mechanisms of functional changes in the brain are not yet clear. Recent studies suggest that the brain's reconfiguration efficiency appears to be a key feature of its network dynamics and general cognitive abilities. In this study, we compared the association between rehabilitation effects and reconfiguration efficiency.Methods We evaluated CLP patients with speech rehabilitation (n = 23) and without speech rehabilitation (n = 23) and normal controls (n = 25). Assessed CLP patients on the Chinese Speech Intelligibility Test Word Lists and collected fMRI data and behavioral data for all participants. We compared behavioral data and task activation levels between participants for between-group differences and calculated reconfiguration efficiencies for each task based on each participant. In patients, we correlated reconfiguration efficiency with task performance and measured the correlation between them.Results Behaviorally, CLP patients with rehabilitation scored significantly higher than those without rehabilitation on the Chinese Speech Intelligibility Test Word Lists. Rehabilitation caused local brain activation levels of CLP patients to converge toward those of controls, indicating rehabilitative effects on brain function. Analysis of reconfiguration efficiency across tasks at the local and whole-brain levels identified underlying recovery mechanisms. Whole-brain reconfiguration efficiency was significantly and positively correlated with task performance.Conclusion Our results suggest that speech rehabilitation can improve the level of language-related brain activity in CLP patients, and that reconfiguration efficiency can be used as an assessment index of language clarity to evaluate the effectiveness of brain rehabilitation in CLP patients, a finding that can provide a better understanding of the degree of brain function recovery in patients.