Magnetic navigation provides contact-free and line-of-sight-independent feedback for robotic systems, yet existing approaches typically rely on explicit pose estimation or direct use of raw magnetic measurements, making accurate control susceptible to modeling errors, measurement noise, and disturbances. This work presents MagServo, a hierarchical learning-based framework for robust 6-DoF magnetic servoing directly using the learned latent magnetic feature. MagServo learns uncertainty-resilient magnetic representations through masked reconstruction and captures state-dependent interaction dynamics between robot motion and latent magnetic transitions without analytical magnetic models or explicit Jacobian supervision. Based on the learned dynamics, a hierarchical controller combines nonlinear model predictive control for coarse approach with local Jacobian inversion for precise fine regulation. Extensive physical experiments demonstrate submillimeter and subdegree accuracy, achieving mean terminal errors of 0.386 mm and 0.479 degree for 6-DoF pose reaching. MagServo further outperforms a localization-based control baseline in complex trajectory tracking and maintains robust performance under unseen magnetic-source configurations without retraining. A supplementary video of the real-robot experiments is available at https://youtu.be/rZt1NUP1Mr0.

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