Subcortical morphological abnormalities are associated with cognitive impairment in schizophrenia. We hypothesized that patients with different degree of cognitive impairment might be separated by subcortical morphological abnormalities. Here we identified two distinct clusters in patients with schizophrenia based on their regional subcortical volume. Different degree of regional subcortical volume, global brain volume and cognitive impairment were observed between two clusters of patients, with more severe cognitive impairment in the more severe morphological deficit cluster. These findings indicate critical relationships between subcortical structures and cognition in schizophrenia, and suggest that subcortical morphological abnormalities could help to capture cognitive profiles in schizophrenia.