Cleft lip and palate (CLP) may induce alterations in functional connectivity (FC) throughout the whole brain, potentially leading to speech dysfunctions; however, the precise neurobiological mechanisms involved remain unknown. This study aimed to systematically examine the consequences of neurological impairments associated with CLP on whole-brain FC and speech functionality. A total of 33 CLP individuals and 41 control participants were included in this study. Eight meaningful brain networks were identified through independent component analysis (ICA). The intergroup differences and correlations with speech scores for both intranetwork and internetwork FC were calculated. We observed decreased FC within the sensorimotor network (SMN), default mode network (DMN), and cerebellar network (CN) and increased FC within the executive control network (ECN). Additionally, FC was enhanced between the SMN and the auditory network (AN), attention network (ATN), and salience network (SAN); between the DMN and the visual network (VN) and ECN; and between two independent components of the DMN. Furthermore, significant correlations were observed between altered FC and speech assessment scores. Our research demonstrated that brain plasticity in CLP individuals with speech deficits involves widespread changes in brain connectivity, significantly improving our understanding of the neural basis of speech impairment in CLP individuals.