Brain alterations associated with illness severity in schizophrenia remain poorly understood. Establishing linkages between imaging biomarkers and symptom expression may enhance mechanistic understanding of acute psychotic illness. Constructing models using MRI and clinical features together to maximize model validity may be particularly useful for these purposes. A multi-task deep learning model for standard case/control recognition incorporated with psychosis symptom severity regression was constructed with anatomic MRI collected from 286 patients with drug-naïve first-episode schizophrenia and 330 healthy controls from two datasets, and validated with an independent dataset including 40 first-episode schizophrenia. To evaluate the contribution of regression to the case/control recognition, a single-task classification model was constructed. Performance of unprocessed anatomical images and of predefined imaging features obtained using voxel-based morphometry (VBM) and surface-based morphometry (SBM), were examined and compared. Brain regions contributing to the symptom severity regression and illness identification were identified. Models developed with unprocessed images achieved greater group separation than either VBM or SBM measurements, differentiating schizophrenia patients from healthy controls with a balanced accuracy of 83.0% with sensitivity = 76.1% and specificity = 89.0%. The multi-task model also showed superior performance to single-task classification model without considering clinical symptoms. These findings showed high replication in the site-split validation and external validation analyses. Measurements in parietal, occipital and medial frontal cortex and bilateral cerebellum had the greatest contribution to the multi-task model. Incorporating illness severity regression in pattern recognition algorithms, our study developed an MRI-based model that was of high diagnostic value in acutely ill schizophrenia patients, highlighting clinical relevance of the model.