To develop effective medical care and therapeutic control using an artificial heart, a new control method has been developed. This new method can control the artificial heart effectively and can adapt to internal physiological behavior using measured physiological data; aortic pressure, aortic flow, and pump flow. This method consists of first, a second-order physiological model, which represents the internal physiological behavior by a mathematical equation; and second, an estimation method, which can identify the physiological parameters; aortic inertia, aortic resistance, aortic compliance, and peripheral resistance by a parameter identification method. It can then calculate the resonant frequency as the control signal for the artificial heart from the identified physiological model. To confirm the effectiveness, the proposed method was evaluated in a computer simulation study. This evaluation showed that the new method could estimate the physiological parameters and the resonant frequency within a 10% error. The impedance of the systemic circulation could also be reduced by this method.