Transcranial Magnetic Stimulation (TMS) has been widely used in clinical neuroregulation fields such as improving brain cognitive function because of its ability to non-invasibly detect and modulate the excitability and function of the cerebral cortex. The functional realization of working memory requires the synchronous activity of multiple brain regions. In this paper, it is of great significance to combine behavioral and electrophysiology, establish causal network connections across brain regions, and explore the regulatory mechanism of different modes of TMS on brain cognitive function from the perspective of memory-related brain regions. Firstly, repetitive Transcranial Magnetic Stimulation (rTMS) and intermittent Theta Burst Stimulation (iTBS) are performed in aged Wistar rats, a blank control group is established at the same time, and the Local Field Potentials (LFPs) are collected by an in vivo multichannel microelectrode array during a working memory task. Then, the LFPs brain causal network is constructed based on the directed transfer function. Finally, by comparing the behavioral results and the causal network parameters of each brain region, the effects of TMS on the working memory behavior and the information synergy between brain regions are explored. The results show that the average number of days that rats in the rTMS and iTBS groups performed the correct working memory task is reduced, and the average correct rate is higher than that in the blank control group. After stimulation, the bidirectional network connectivity between prefrontal lobe and hippocampus in the rTMS group and the iTBS group is significantly enhanced, and the strength of information flow and causal streamability are significantly improved (P < 0.05). Therefore, both rTMS and iTBS can promote the communication between the hippocampus and prefrontal cortex, thereby improving the working memory ability of aged rats.