The Organic Rankine Cycle System is an effective approach for recovering the engine exhaust thermal energy. The physical characteristic of the Rankine fluid is the key factor for the capacity and the stability of the expander power output. In the research, the influences of the evaporator organic medium state and flow rate on the expander power output are fully analyzed for the sufficient utilization of the waste thermal energy. Firstly, the exhaust characteristics of the diesel engine were processed by the data of the bench test. Then, the integral mathematical model of the Organic Rankine Cycle was built. Based on the comparison for the 2-zone and 3-zone evaporator, the influence for expander output are analyzed especially emphasis on the factors of engine working condition, the flow rate, temperature and state of Rankine fluid. The result shows that the thermal energy recovery efficiency could be optimized by the matching for engine and ORC system and the precise control of the physical state of the ORC Rankine fluid.