For the insufficient thermal efficiency of highly-efficient special hybrid engine, the thermodynamic model was corrected by using the test data, the quantitative evaluation of problem was conducted, and then the optimized scheme of thermal efficiency was put forward. The results show that the slow combustion rate, poor antiknock performance, and low compression ratio of prototype are the reasons of non-reaching level thermal efficiency. The optimized scheme includes optimizing the combustion system, increasing the compression ratio to 12, and increasing the height of the intake and exhaust lifts. According to the optimization results, the average fuel consumption under partial load  reduces by 4.4%. In addition, the minimum fuel consumption is 209 g/（kW·h）, the corresponding thermal efficiency is 40.5%, which meets the design target. The Miller cycle and cooling EGR technology needs to match the rapid combustion system.