Background The aim of this study was to investigate the correlation and gender differences between cognition and suicidal tendency in patients with schizophrenia.Methods A total of 554 patients with schizophrenia were recruited. The Mini-Mental State Examination (MMSE), Positive and Negative Syndrome Scale (PANSS), Interpersonal Reactivity Index (IRI), Toronto Alexithymia Scale (TAS), and Insomnia Severity Index (ISI) were used to assess clinical symptoms.Results In male patients, MMSE score and the incidence of suicidal tendency were correlated (P = 0.04, OR = 1.06, 95%CI: 1.00-1.12). Among patients with cognitive dysfunction, IRI score (P = 0.01, OR = 1.04, 95%CI: 1.01-1.06), and types of antipsychotic drugs (P < 0.01, OR = 3.97, 95%CI: 1.76-8.97) in male patients were associated risk factors for suicidal ideation. Among patients without cognitive dysfunction, PANSS positive subscale score (P = 0.03, OR = 1.06, 95%CI: 1.01-1.11), and PANSS general psychopathology score (P = 0.02, OR = 1.05, 95%CI: 1.01-1.08) were associated risk factors for suicidal ideation in male patients and PANSS positive subscale score (P < 0.01, OR = 1.15, 95%CI: 1.05-1.26) were associated risk factors for suicidal ideation in female patients.Conclusions There were significant gender differences in the correlation between cognitive functioning and suicidal ideation in patients with schizophrenia. Cognitive function may play an important mediating role in other factors on suicide.