Stimulating specific brain regions has been found useful for treating neural disorders, such as the Parkinson's disease, epilepsy, depression, etc. However, how electrical stimulation modulates neural activities remains not fully understood. As animal models provide the advantage of recording and stimulating different disease-related regions simultaneously, this paper introduces the latest development of a multisite, closed-loop-controlled microsystem for investigating novel treatments on neural degenerative diseases with freely-moving rats. The algorithms for recognizing pathological neural activities automatically are also developed and realized in hardware, so as to control the stimulation in a closed loop and in real time. The pilot studies on the efficacy of treating the Parkinson's disease with closed-loop-controlled stimulation will be presented and discussed. Finally, the feasibility of modelling and probing how neural dynamics and connectivity are modulated by stimulation will be an important topic for future research.