Magnetic-based driving applications are receiving increasing attention. This study proposed a novel reciprocating permanent magnetic actuator (PMA) to manipulate magnetic micro robots to impact and clear blockages inside fluid pipes in a linear path. The PMA consisted of a cylindrical permanent magnet and a crank slider structure. A straight pipe with a circular cross-sectional area was located in front of the actuator to study the driving performance of PMA. A micro permanent magnet with a cylinder shape was employed as a working robot for manipulation inside the pipe. Firstly, analytical formulas were derived to obtain the magnetic driving force acting on the micro robot and determine the most suitable magnet configuration. The finite element simulation verified the analytical calculation. The developed reciprocating PMA prototype was then introduced, and the PMA and micro robot’s motion performance was analysed. Lastly, preliminary experiments were carried out for evaluating the micro robot’s motion characteristics. Performance tests for different excitation frequencies, flow rates, viscosities, and axial distances, indicating that PMA could manipulate the magnetic micro robot inside the pipe. The results confirmed that the developed PMA could effectively drive the micro robot with the advantage of consecutive magnetic driving. Especially, the micro robot featured good flexibility, rapid response, and a simple structure, suggesting that this micro robot may play an important role in industrial and medical applications, such as blockage elimination and thrombus clearance.