Purpose This study aimed to investigate the early functional connectivity alterations between insula subdivisions and other cortical regions in patients with acute mild traumatic brain injury (mTBI) and subsequently to explore the relationship between functional connectivity changes of insula subdivisions with other cortical regions and cognitive function. Methods Fifty-three mTBI patients and 37 age-, gender- and education level- matched healthy controls were included in this study. All participants obtained resting state functional magnetic resonance imaging (rs-fMRI) and clinical and neuropsychological evaluations (Montreal cognitive assessment, MoCA) at the acute stage. Functional connectivity alterations of insula subdivisions and correlations with MoCA were further explored by seed-voxel functional connectivity. Results Compared with healthy controls, patients with acute mTBI showed significantly decreased functional connectivity between the L-vAI and the left middle temporal gyrus and right superior frontal gyrus and significantly decreased functional connectivity between the R-vAI and the right middle frontal gyrus and right hippocampus. While significantly decreased functional connectivity were observed between the L-dAI and the right superior frontal gyrus. In addition, significantly increased functional connectivity was observed between the R-PI and the left inferior frontal gyrus. Furthermore, the mTBI group demonstrated positive correlations between performances in orientation and insula and middle temporal gyrus and superior frontal gyrus and middle frontal gyrus functional connectivities. Abstraction scores for mTBI patients positively correlated with functional connectivity between insula and middle frontal gyrus. Conclusions The present study demonstrated functional connectivity dysfunction of insula subdivisions and correlations between these alterations and cognitive performance, which provide a novel insight into the neurophysiological mechanism of cognitive impairment in patients with mTBI at the acute stage.