Repetitive transcranial magnetic stimulation (rTMS) has been increasingly used for its potential treatment effects across diverse mental disorders. However, the treatment effect is elusive and the rate of positive responders is not high, which make it in great demand of optimizing rTMS protocols to improve the treatment effects and the rate. In this regard, neural activity guided optimization has indicated great potential in several neuroimaging studies. In this paper, we present our ongoing work on optimizing rTMS treatment of a balance disorder, i.e., Mal de Debarquement syndrome (MdDS), by investigating treatment-related EEG neural synchrony and functional connectivity changes. Motivated by our previous pilot study of rTMS on MdDS, we firstly applied a bilateral dorsolateral prefrontal cortex (DLPFC) rTMS protocol to evaluate its efficacy and the treatment-related neural responses via an independent component analysis (ICA)-based framework. Thereafter, guided by identified EEG neural synchrony and functional connectivity patterns, we proposed three potential stimulation targets covering posterior nodes of the default mode network (DMN), and implemented a new rTMS protocol by stimulating the target with the great symptoms relief. The preliminary clinical response data has indicated that the new rTMS protocol significantly increase the rate of positive responders and the degrees of the improvement. The present study demonstrates that it is promising to integrate EEG neural synchrony and functional connectivity into the optimization of rTMS protocols for different mental disorders.