It is well known that indirect injection (IDI) diesel engines have better exhaust performance but lower fuel economy than direct-injection (DI) diesel engines. In recent years, fuel efficiency has been strongly demanded to reduce global warming. Therefore, the IDI engine is required to reduce fuel consumption. According to past research, fuel injection control can be one of the means to improve fuel efficiency in the IDI system. This paper tried to apply two-stage fuel injection as one of the fuel injection control methods to improve fuel efficiency while suppressing exhaust emissions. Particularly, since it is considered necessary to reduce the amount of injection during the ignition delay period in the sub-chamber with the IDI type, two-stage injection with a small amount of pilot injection was applied. In the study, engine tests were first conducted by changing the injection timing with single-stage injection, and then, the heat generation processes were analyzed to understand the combustion characteristics that are important for improving fuel efficiency and exhaust performance with IDI diesel combustion. Based on these analyses, pilot injection was applied as a means of controlling combustion characteristics to improve fuel economy and exhaust emissions. As a result, it has been shown that if two-stage injection with a small amount of pilot injection is used in place of single-stage injection, combustion with a shortened combustion period is possible. This combustion can avoid delay of the end of combustion while suppressing the initial combustion, thereby improving fuel efficiency. Especially when the main injection timing is delayed later than that of single-stage injection, fuel injection can be performed without delaying the end of main injection due to pilot injection. Therefore, in this case, the increase in THC and PM is suppressed in addition to the improvement of fuel efficiency and the NOx emission is also reduced.