Objective: To investigate structural and functional alterations of gray matter (GM) and examine their clinical relevance in neuromyelitis optica (NMO) using multimodal magnetic resonance imaging (MRI) techniques. Methods: A total of 35 NMO and 36 healthy controls (HC) were recruited in this study. Cortical lesions were investigated by double inversion recovery technique. Five voxel-wise MRI measurements were obtained for each participant in the GM including gray matter volume (GMV), fractional anisotropy (FA), mean diffusivity (MD), amplitude of low-frequency fluctuation (ALFF), and weighted functional connectivity strength (wFCS). Between-group differences, cross-modality relationships, and MRI-clinical correlations were examined. Results: No cortical lesions were found in NMO. Compared to HC, NMO patients exhibited significantly decreased GMV in deep GM and cortical regions involving visual function and cognition. Diffusion GM abnormalities were widespread in the patients. Decreased ALFF and wFCS were observed in the patients in sensorimotor, visual, cognition, and cerebellar sites. GM structural alterations were correlated with cognitive but not physical disability scores of the patients. Conclusion: Despite the lack of focal cortical lesions, patients with NMO exhibit both structural and functional alterations of GM in cerebrum and cerebellum that predominantly involve deep GM, visual, motor, and cognitive regions. GM alterations are associated with cognitive impairment but not physical disability.