Multi-processor system-on-chip (MPSoC) simulators are many orders of magnitude slower than the hardware they simulate due to increasing architectural complexity. In this paper, we propose a new application sampling technique to accelerate the simulation of MPSoC design space exploration (DSE). The proposed technique dynamically combines simultaneously executed phases, thus generating a sampling unit. This technique accelerates the simulation by allowing the repeated combinations of parallel phases to be skipped. A complementary technique, called cluster synthesis, is also proposed to improve the simulation acceleration when the number of possible phase combinations increases. Our experimental results show that this technique can accelerate the simulation up to a factor of 800 with a relatively small estimation error.