Background <p>Schizophrenia is marked by disruptions in functional connectivity; however, findings on the specific brain regions involved and the direction of connectivity changes remain inconsistent. Therefore, a more comprehensive framework that evaluates whole-brain functional connectivity is needed to better understand brain dysfunction and its relationship to symptoms. This study aims to investigate whether the primary gradient in schizophrenia patients differs significantly from that in healthy controls using recently developed gradient-based analysis.</p> Methods <p>We applied a gradient analysis to resting-state fMRI data to characterize the sensorimotor-to-transmodal functional cortical organization in schizophrenia patients (<i>n</i> = 32) and healthy controls (<i>n</i> = 27). We also used correlation analysis to examine the relationship between primary gradient organization and PANSS positive, negative, general subscale scores and total scores of SANS in schizophrenia patients.</p> Results <p>The gradient analysis demonstrated that, compared with the healthy controls, schizophrenia exhibited reduced sensorimotor-to-transmodal differentiation in which there is increased gradient values from the sensorimotor systems of the cortical organizations such as visual network and decreased gradient values from the higher-level systems such as salience network and frontoparietal network. Alterations in primary gradient organization were significantly associated with PANSS positive and negative subscales, and total scores of SANS in schizophrenia.</p> Conclusion <p>The results indicate that schizophrenia exhibits disrupted cortical functional organization, and this arises from the reduced differentiation within the sensorimotor-to-transmodal gradient. These alterations in the sensorimotor-to-transmodal gradient explains variability in some of the clinical symptoms of schizophrenia.</p>