Nowadays, with the development of semiconductor technology and the requirement of the diversification of applications, heterogeneous multi-core processors have been widely used in high-performance embedded systems. How to manage and distribute the available resources (such as processing cores) during running in order to meet the requirements in performance and power consumption of the system and the applications that the system runs is a main challenge that the system focuses. However, although some mainstream resource management techniques have achieved good results in terms of performance and/or power consumption optimization, they lack the strict reliability guarantee for the resource management component. Therefore, a method based on Discrete Controller Synthesis (DCS) was proposed to automatically and reliably design the online resource management scheme for heterogeneous multi-core systems, which applies DCS (which is formal and can construct management control components automatically) to the design of online resource management components for heterogeneous multi-core systems. In this method, the heterogeneous system’s running behaviors (such as how to distribute the processing cores to the applications) were described by using the formal models, and the online resource management problem was transformed to a DCS problem aiming at one system management objective (such as maximizing system performance). On this basis, the existing DCS tools were used to illustrate and validate the proposed method, and the scalability of the DCS method was evaluated.