Common rail injection system has great flexibility in injection timing, pressure and multi-injection compared with other injection systems, many studies and applications have reported the advantages of using common rail system to meet the strict emission regulation and to improve engine performance for diesel engines [1-2] *.The purpose of this study was aimed to understand the effect of pilot injection on NOx and soot when pilot injection was used to reduce combustion noise. A single cylinder high-speed diesel engine with common rail system was used to acquire the data of interesting such as exhaust emissions, in-cylinder pressure and combustion noise level (CNL). To study the complex effect of pilot injection with EGR, cooled EGR was used as well. Together with engine testing, a transparent engine was used to find more details by comparing combustion process and a simulation was carried out to estimate the result of desired pilot.As a result, based on the trade-off for NOx, soot and combustion noise, the effect of pilot injection under different engine loads, EGR has been discussed. Meanwhile, the information from combustion process and simulation has indicated the problems existed in current system and the direction to make further improvement.