Microscopy has been an indispensable tool for micro/nanosample imaging, manipulation, and characterization. However, viewing the micro/nanosample from multidirection is still a big challenge for current microscopy. To address the above issue, this paper proposes a novel nanorobotic manipulation system for the automatic alignment and multidirectional imaging under microscopes. First, a miniature rotation robot with three degrees of freedom is designed and integrated with a microscope. Then, a forward-backward alignment strategy containing three loops, i.e., position shift loop, angle loop, and magnification loop, is proposed to align the sample to the rotation axis of the robot automatically. After that, the sample is imaged from multidirection by rotating the robot with one revolution (360°). Finally, the alignment accuracy is evaluated and multi-directional images of various samples are implemented. This study provides a new way for the microscopic imaging, which is expected to exert a significant impact in multiple fields on a small scale, including microscopy imaging, microdefect detection, micromanipulation, in situ characterization, and so on.