Scheduling threads in a system with many cores includes generating a thread map where a connection relationship between a plurality of threads is represented by a frequency of inter-process communication (IPC) between threads, generating a core map where a connection relationship between a plurality of cores is represented by a hop between cores, and respectively allocating the plurality of threads to the plurality of cores defined by the core map, based on a thread allocation policy defining a mapping rule between the thread map and the core map.