Objective As a new type of transcranial magnetic stimulation, the intermittent theta burst stimulation (iTBS) has been widely used to explore brain cognitive function and neuroregulation, but its electrophysiological regulation mechanism is still unclear. Therefore, exploring the underlying electrophysiological mechanism and the effect of iTBS on the brain’s cognitive functions is of great significance for the treatment of brain diseases and clinical application of magnetic stimulation.Methods In this study, the model rats were treated with iTBS, and the local field potential (LFPs) signals in the ventral hippocampus (vHPC) and medial prefrontal lobe (mPFC) were collected and recorded during the working memory (WM) tasks in rats. The effect of iTBS on neural network coordination and information interaction across brain regions was investigated by using Granger causality network.Results The results suggested that iTBS enhanced the WM ability and the behavioral performance of the rats, reducing the time to complete the WM task by (2.67±1.63) d (P<0.05). At the same time, iTBS enhanced the self-causal network connections in vHPC and mPFC during WM, and increased the network connection strength, connection density and global efficiency (P<0.05). In addition, iTBS enhanced the cross-brain network connection between vHPC and mPFC, and increased the node degrees and causal flow (P<0.05) from vHPC to mPFC.Conclusion iTBS has a significant positive effect on the behavior of WM and neural network in related brain areas of rats. iTBS can promote the cognitive ability of rats and improve the efficiency of information interaction and transmission of neural network. The neural regulation mechanism of iTBS may be to enhance the WM ability by enhancing the network connection and information interaction between vHPC and mPFC.