Functional/metabolic changes in different brain regions of interest are of importance for better understanding of the pathophysiological mechanism underlying the human brain diseases. In this work, we present a novel design of the dual-channel 31P MRS system for simultaneous measurements of cerebral high-energy phosphate metabolism from two brain regions of interest by incorporating a new pulse sequence and two separated RF surface coils with a transistor-transistor logic (TTL) controller. By successfully implementing this method, we are able to obtain high quality in vivo 31P MR spectra from both frontal and occipital lobes within the same amount of time as the traditional method covering one brain region. From an engineering perspective, this new approach provides a cost-effective solution for in vivo 31P MRS study of multiple brain regions with a conventional single-channel transmitter-receiver configuration. Therefore, this valuable MR tool can be used in examining the cerebral energy metabolism across different brain regions, and the same approach could be employed to other spin applications.