Abstract Purpose Individuals with convergence insufficiency (CI) encounter challenges in turning their eyes inward during near work. It is unclear how this relates to brain structural and functional alterations. This study aimed to explore the neural mechanism underlying CI using multimodal brain magnetic resonance imaging (MRI). Methods Thirty‐four CI participants and 35 healthy controls (HC) were recruited, who underwent visual examinations and brain MRI scanning. Structural MRI data were analysed to calculate cortical thickness, volume and surface area. Fractional amplitude of low‐frequency fluctuation (fALFF) and seed‐based functional connectivity were obtained from resting‐state functional MRI data. The brain structural and functional metrics were compared between the two groups followed by correlation analyses between clinical measurements and significant brain features. Results Relative to HC, individuals with CI had lower grey matter volume (GMV) and surface area in the right frontal eye fields, parietal eye fields and left medial orbitofrontal cortex, higher GMV and surface area in the right middle frontal and inferior temporal gyri and higher fALFF of the left cerebellum and functional connection between bilateral cerebellums. GMV of the right middle frontal gyrus and fALFF in the left cerebellum were positively correlated with the near point of convergence in all participants. Conclusions Lower structural metrics in the visual and oculomotor cortices and higher functional activity in the cerebellum may underpin convergence dysfunction and visual fatigue, while higher structural metrics in the right middle frontal and inferior temporal gyri reflect partial compensation for the visual and oculomotor cortex defects, thereby maintaining attention and parallax information processing. This study may enhance understanding of the neural mechanism of CI by revealing the impact of abnormal visual experiences of CI on the brain with disassociated structural and functional alterations in the vergence system.