In this work, we study the optimal parameter design and microrobotic navigation control of the parallel-mobile-coil system (PMCS) that consists of three mobile electromagnetic coils. With motion driven by a parallel mechanism, the three coils can move in 3D large space and keep as close as possible to the controlled microrobot for magnetic actuation. Although promising for microrobotic applications, how to design such a type of system for a specific workspace requirement is untackled. Regarding this issue, we propose a computational design method, by which one can calculate the structural parameters of a PMCS starting from a required cylindrical workspace. With the derived performance metrics for motion actuation and magnetic actuation of the PMCS, the system actuation performance (composed of motion and magnetic actuation) is optimized. Utilizing the design method, we optimally construct a prototype PMCS for microrobotic navigation. We then conduct experiments to validate the demanding field/force generation capability of the PMCS and demonstrate the navigation control of different types of magnetic microrobots. In particular, we design closed-loop motion controllers for both torque and force-driven microrobots, using which automated large-workspace and high-accuracy trajectory tracking is realized. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —This work is motivated by the recent wide interest in magnetic microrobots. Driven by external magnetic fields, magnetic microrobots can navigate in a wireless manner for targeted delivery/therapy. To promote microrobot applications to the human body, a magnetic actuation system with large workspace is desirable. However, due to the fast decay of magnetic field, the commonly used stationary coil-based magnetic actuation systems have the workspace scalability problem. Thus, several mobile-coil-based systems have been designed. In this work, we propose an optimal design method for the PMCS, using which one can design a PMCS starting from a cylindrical workspace with performance being optimized. We construct a PMCS prototype with a workspace of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\Phi 230 \times 100$</tex-math> </inline-formula> mm <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$^3$</tex-math> </inline-formula> , and we then study the automated microrobotic navigation control methods for the PMCS. Controllers are designed for different types of magnetic microrobots, and experiments show that, using the controllers, the PMCS can perform automated large-workspace microrobotic navigation control with high accuracy.