We propose an extended model of cardiovascular regulation to assess heart rate variability in patients poisoned with organophosphate during their treatment with mechanical ventilation. The model was modified to fit a population of 21 patients poisoned with organophosphorus compounds and undergoing mechanical ventilation. The extended model incorporated the respiratory muscle activity measured by surface electromyography for quantifying the vagal-sympathetic engagement during spontaneous breathing test. The order and structure of the parasympathetic and the sympathetic transfer function with respect to the original model were modified to a second-order system. In this extended model, the parameters related to the vagal-sympathetic response (corner frequency and constant gain) were correlated with respiratory muscle activity. When the diaphragm's contractions were stronger, the sympathetic corner frequency increased while the parasympathetic corner frequency and gain decreased. Thus, the proposed model could be useful to improve the ventilatory support and pharmacological treatment for patients poisoned with organophosphorus compounds considering the vagal-sympathetic response inferred from the respiratory muscle activity.