Although the brake thermal efficiency and exhaust emissions performance of the engine have been improved significantly in recent years, these issues are still not fully-resolved. Natural gas (NG) engine has been widely concerned because of its extensive resources and relatively clean. To better understand the effect of the pilot diesel injection timing on the combustion phases of the pilot diesel and the natural gas, a detailed study was conducted by experiment and numerical simulation. A 6-cylinder turbocharged intercooler diesel/natural gas dual fuel heavy-duty engine was used in this study, and the pilot diesel injection timing was controlled over a very wide range at a constant engine speed of 1335 r/min. The results show that the injection timing has an obvious effect on the engine combustion process including combustion phases of the pilot diesel and the natural gas, and which decide the engine thermal efficiency and exhaust emissions level. The chemical reaction of diesel and natural gas before combustion start at the same time, however, the combustion duration of natural gas lags behind that of diesel. In addition, during the combustion overlap period, the in-cylinder combustion is good and the working ability is strong. To advance the pilot diesel injection timing from 5 °CA BTDC to 35 °CA BTDC, the chemical ignition delay of diesel shows a lengthening trend, and the combustion duration shows a shortened trend. With advancing the pilot diesel injection, the natural gas combustion duration shows a shortened trend, and the shortest is near to 16.5 °CA. There is a clear correspondence between the lengths of combustion period of two fuels. Either the combustion duration or the combustion overlap period shows a shortened trend, but the ratio of the combustion overlap period to the combustion duration is increasing with advancing the pilot diesel injection. The shortest combustion duration corresponds to the lower brake specific energy consumption and emissions.