Magnetic resonance imaging (MRI) systems, outfitted with internal gradient coils capable of manipulating magnetic gradients in three-dimensional (3D) space, offer an intriguing platform for the navigation of medical magnetic robots. These robots offer considerable promise for applications in minimally invasive therapy, targeted drug delivery, and theranostic interventions. However, an MRI-driven robot presents a challenging contradiction between real-time control and image resolution, resulting in suboptimal tracking accuracy—attributed to the inefficiency of conventional signal acquisition and the presence of metal artifacts. In this paper, we report a multi-frequency excitation sequence with dual-echo (MFDE) that reduces the repetition time (TR) to 30 ms, allowing the precise tracking of magnetic particles (relative error < 1%) without artifacts. The duty cycle of the driving gradient is as high as 77%, and perturbations from the imaging gradients are eliminated. Expanding on these foundations, we adapted our technique to 3D operations. We established an integrated platform for imaging and motion control by creating a three-view window and developing a control joystick to be used in conjunction with the platform. Demonstrations of navigation in a maze, in a phantom vessel, and in vivo animal trials validate its feasibility and effectiveness, providing a significant advancement in the field of MRI-guided magnetic robot control.