Provided is a parallel program execution method in which in order to reflect structural characteristics of a multithreaded processor-based parallel system, performance of the parallel loop is predicted while compiling or executing using a performance prediction model and then the parallel program is executed using an adaptive execution method.The method includes the steps of: generating as many threads as the number of physical processors of the parallel system in order to execute at least one parallel loop contained in the parallel program; by the generated threads, executing at least one single loop of each parallel loop; measuring an execution time, the number of executed instructions, and the number of cache misses for each parallel loop; determining an execution mode of each parallel loop by determining the number of threads used to execute each parallel loop based on the measured values; and allocating the threads to each physical processor according to the result of the determination to execute each parallel loop.The method significantly improves the performance of the parallel program driven in the multithreaded processor-based parallel system.