Schizophrenia has been associated with autonomic dysregulation and increased cardiovascular co-morbidity. We hypothesised that autonomic dysregulation in patients with schizophrenia is associated with psychopathology and metabolic profiles. In this study, we aimed to evaluate psychopathology, comprehensive metabolic profiles and cardiac autonomic function using heart-rate variability (HRV) analysis in patients with schizophrenia. A total of 94 patients with schizophrenia and 51 healthy controls were recruited. Each patient underwent a physical examination, laboratory tests and rating scale evaluation, and all subjects underwent a 1-h electrocardiogram monitoring. Analysis of variance was used to compare demographic and HRV variables between control and patient groups. We applied multiple regression analysis with backward selection to examine the association between HRV indices and demographic, metabolic and psychopathology profiles. A decreased HRV was found in patient groups, compared to controls. Reduced vagal-related and complexity domain of HRV indices in patient groups were correlated with increased body mass indices, diastolic pressure, triglycerides, high- and low-density lipoprotein and severity of psychosis mainly in the negative symptom domain. This study provides evidence that altered autonomic function is associated with both psychopathology and metabolic profiles in patients with schizophrenia. These findings may warrant future research in using HRV as objective markers to monitor cardiovascular health and the severity of psychosis in patients with schizophrenia.