The invention discloses a microprocessor micro system structure parameter optimization method based on a Petri network. The method comprises the following steps that a template of a flow line model is built on the basis of the colored Petri network, an instruction sequence of a target application program is obtained, relevant information between the instructions and the function unit types is obtained, a colored Petri network model, running under the current parameter configuration, of the target program is generated, a Petri network simulation tool is used for simulation, a simulation report is generated, the colored Petri network model is used for generating a corresponding directed acyclic graph according to the simulation report, a key path of the directed acyclic graph and nodes passed by the key path are calculated, the release time of each entering edge of each node is calculated, the performance bottle neck or power consumption bottle neck for running the target application program by the microprocessor in the current micro system structure parameter configuration is analyzed, and if the optimization is required, the micro system structure parameters are regulated. The microprocessor micro system structure parameter optimization method has the advantages that the prediction reliability and the precision are high, the searching design space relating range is wide, the optimization algorithm complexity is lower, and the optimization is fast and efficient.