In the microfluidic applications, viscous-driven pumping mechanism is a promising one since the viscous effect increases significantly as the size of device decreases, relative to the inertial effect. However, there exist a few drawbacks we have to improve such as low efficiency and small volume flow rate. In the present study, an optimum design synthesis is proposed to enhance the performance characteristics of the micropump with single rotating cylinder. First, the unstructured grid CFD method is described and validated by comparing its results to the previous results. Next, an automated optimum design synthesis tool is constructed by combining the aforementioned CFD analysis model with the mathematical optimization model. This technique is used to improve the performance characteristics of newly designed viscous-driven pump. The presented results show that the fluid dynamic optimization tool is robust and may be applied to other microfluidic device design applications.