Implantable ventricular assist devices (iVADs) are used for severe heart failure therapy. A flow rate estimation method is required for adequate control of the blood pump flow rate without using a flow meter in iVAD therapy. We developed a flow rate estimation method using the eccentric position of a magnetically levitated (maglev) impeller determined by radial passive stability. This estimation method meets clinical requirements because of high estimation accuracy even under varying blood viscosity (pump Reynolds number, Re_p). In this study, a computational fluid dynamics (CFD) analysis was performed to clarify the basis of the maglev impeller passive stability, aiming at clinical application of this method. First, no significant variation in the pump pressure distribution, which determined the impeller’s passively stabilized position, was observed under typical blood pump operating conditions (Re_p = 35000–63000). In contrast, the working fluid density change affected the estimation accuracy by changing the pump characteristics. However, its effect on the estimation accuracy was less than 1% because the blood density can only change within a narrow range. These results indicate that the estimation method can be applied to other devices with a passively stabilized impeller. Additionally, CFD analysis indicates that the variation in the pump flow path design based on radial clearance can change the impeller radial position, the radial hydraulic force exerted on the impeller, and its magnitude with respect to the pump flow rate. The CFD results suggest that the resolution of the method can be adjusted by changing the flow path design of the radial clearance. However, the radial hydraulic fluid direction was almost constant in the radial clearance range of 1.0–3.0 mm. Therefore, the variation in the impeller radial position direction with respect to the pump flow rate did not change significantly with the radial clearance design under the present analysis conditions. However, the rate of variation in the impeller radial position with respect to the pump flow rate, which determines the accuracy of the estimation method, can be adjusted with the radial clearance design. The estimation method, which has remarkable characteristics, evaluated in this research has the potential for use in clinical practice.