The properties of conventionally utilized magnetic cores limit the generation of a strong controllable magnetic force for the manipulation of micro-/nanorobots. This study proposes a novel electro-permanent magnetic actuator having a composite core structure that can significantly improve the magnetic field and field gradient. The core structure, called the composite electro-permanent magnetic actuator (CEPMA), consists of a hybrid permanent magnet sandwiched between an iron core and iron disk with a copper wire wound around it. . The CEPMA creates a strong magnetic field and enables the switching on/off of the magnetic field. A prototype of a magnetic actuator system using six CEPMAs was built with optimal parameters and was capable of 3-dimensional (3D) position control with a maximum achievable field and gradient field of 124 mT and 1.9 T/m, respectively, by utilizing a lower power consumption. We derived a mathematical model and control approach to address its hysteresis property and obtain a current input for the desired magnetic force for precise control of a microrobot. The theoretical analysis and experimental validation of CEPMA indicated that the proposed structure could enhance the controllable magnetic field and gradient field by up to 30% compared to the conventional iron core electromagnet. The system was also tested for 3D manipulating different microrobots in an in vitro environment with high accuracy. The experimental results demonstrate the potential of this newly developed platform for manipulating microrobots with high throughput.