Automatic 3D navigation control of microrobot in large microenvironment is one of the primary challenges hindering its applications. In this article, we present a systematic approach to use an electromagnetic manipulation system to deal with this challenge. Two movable orthogonal microscopic cameras scan the microenvironment on the top view and side view to build a stereo occupancy map automatically. The initial position of microrobot can be located on the basis of the similarity curves generated by the scanning sequences. In accordance with the distribution characteristic of electromagnetic fields in workspace, an enhanced rapidly exploring random tree algorithm is proposed to avoid obstacles in the complex environment. To ensure continuous visual servo in wide range, a field-of-view tracking method is developed using a specific image definition evaluation algorithm. A prescribed performance controller with disturbance observer is designed, which guarantees that the microrobot can remain in the view of microscopic cameras, and the transient and steady-state performance of the system can satisfy the expected requirements. A set of experiments are performed to verify the effectiveness of the proposed automatic 3D navigation strategy. Experimental results show that the microrobot can navigate automatically in a$\boldsymbol{12}\,\times 10\,\times \text{10-mm}$microenvironment containing obstacles, and achieve reliable field-of-view tracking and path following at high speed.