Surface-enhanced Raman spectroscopy (SERS) is a powerful sensing technique capable of capturing ultrasensitive fingerprint signal of analytes with extremely low concentration. However, conventional SERS probes are passive nanoparticles which are usually massively applied for biochemical sensing, lacking controllability and adaptability for precise and targeted sensing at a small scale. Herein, we report a “rod-like” magnetic nanomotor-based SERS probe (MNM-SP) that integrates a mobile and controllable platform of micro-/nanomotors with a SERS sensing technique. The “rod-like” structure is prepared by coating a thin layer of silica onto the self-assembled magnetic nanoparticles. Afterwards, SERS hotspots of silver nanoparticles (AgNPs) are decorated as detecting nanoprobes. The MNM-SPs can be navigated on-demand to avoid obstacles and target sensing sites by the guidance of an external gradient magnetic field. Through applying a rotating magnetic field, the MNM-SPs can actively rotate to efficiently stir and mix surrounding fluid and thus contact with analytes quickly for SERS sensing. Innovatively, we demonstrate the self-cleaning capability of the MNM-SPs which can be used to overcome the contamination problem of traditional single-use SERS probes. Furthermore, the MNM-SPs could precisely approach the targeted single cell and then enter into the cell by endocytosis. It is worth mentioning that by the effective mixing of intracellular biocomponents, much more informative Raman signals with improved signal-to-noise ratio can be captured after active rotation. Therefore, the demonstrated magnetically activated MNM-SPs that are endowed with SERS sensing capability pave way to the future development of smart sensing probes with maneuverability for biochemical analysis at the micro-/nanoscale.