Network physiology aims to define healthy and diseased states by analysing structural, dynamical and regulatory alterations of the interaction in physiological systems and sub-systems and is getting more and more into the focus of interest in medicine. In this study, we quantified and characterized how different antipsychotics influence central-cardiorespiratory network (CCRN) pathways in 17 patients suffering from paranoid schizophrenia (SZO) treated with depot antipsychotic medication (SZO1: 77% atypical neuroleptics, SZO2: 23% mixture of antidepressant and atypical neuroleptics) in comparison to 21 healthy subjects applying the normalized short time partial directed coherence approach. From all participants we recorded and pre-processed the continuous heart rate (successive beat-to-beat intervals, BBI), calibrated respiratory inductive plethysmography signal (respiratory frequency, RESP), and a 64-channel EEG (mean power PEEG in relation to each RR-interval) for 15 minutes under resting conditions. We could show a weaker central influence on the cardiac- and respiratory system (PEEG→BBI, PEEG→RESP) in SZO2 than in SZO1 compared to CON, and a stronger respiratory influence on central system (RESP→PEEG) in SZO2 than in SZO1 compared to CON. The central-cardiac coupling (PEEG˗BBI) is weaker pronounced, and the central-respiratory coupling (PEEG˗RESP) is stronger pronounced in SZO2. Particularly the central nerve system controls less the cardiac and the respiratory system in SZO2. This suggests that central-cardiorespiratory regulation processes (closed-loops) are more affected by the mixture of antidepressant and atypical neuroleptics (SZO2) than atypical neuroleptics. Antidepressant and atypical neuroleptics revealed a stronger inhibiting effect on the central nervous system than on the autonomic nervous system (RESP). This study showed that antipsychotics have different effects on the interplay of neuronal and autonomic cardiorespiratory regulatory processes and this knowledge might contribute in future to an optimal selection of therapy strategies in schizophrenia and thus to a more personalised medicine.