Magnetic technology has been a hotspot of neuromodulation research in recent years. However, magnetic coil is limited by their size, and it is impossible to realize precise targeted magnetic stimulation to the target area at the cellular scale. To this end, this study designs a 1 × 4 array micro-magnetic stimulation (μMS) device with four sub-millimeter-sized elements, enabling precise magnetic stimulation of the CA1-CA3-DG tri-synaptic positions in the rat hippocampal region. First, it is determined that 70 KHz/2 mT/1 min magnetic stimulation parameter has a modulatory effect on the long-term potentiation (LTP) of Schaffer-CA1 in rat hippocampus. Then, a 1 × 4 array μMS device is used to perform magnetic stimulation at 70 KHz/2 mT/1 min, targeting the CA1, CA3, and DG regions individually with single-point magnetic stimulation; and multi-region magnetic stimulation is applied to the double-point targeting regions of CA1-CA3, CA1-DG, and CA3-DG, as well as the triple-point targeting region of CA1-CA3-DG, so as to investigate the regulation of LTP by single-region magnetic stimulation and multi-region magnetic stimulation. The experimental results indicate that, in the case of single-region magnetic stimulation, the magnitude of the increase in LTP in the CA1 region is the greatest, followed by the CA3 region, while the effect of magnetic stimulation on the DG region is less pronounced. In multi-region magnetic stimulation, synergistic magnetic stimulation of the three-point CA1-CA3-DG results in a greater increase in LTP compared to stimulation of two individual areas, and the enhancement of LTP induction with multi-region magnetic stimulation surpasses that of single-region stimulation. This study has implications for the collaborative targeted magnetic stimulation application of arrayed micro-magnetic devices.