More emissions are produced when Diesel engines operate in the transient state than in the steady state. This discrepancy is due to mismatching between the air-charging system and the fueling system. Moreover, the difference in the response time between the intake pressure and the exhaust pressure caused by turbo-lag leads to an excess supply of EGR.In this study, a model that can calculate the EGR rate of the intake gas was developed. In the model, temperatures of the air, the EGR gas and the mixture gas were measured with thermocouples which have a fast response. The EGR rate was calculated through the energy balance equation considering heat transfer.Moreover, the estimated EGR rate was applied to a closed-loop control system that receives feedback from 50 % of the mass fraction burned (MFB50) by a 2.2 L Diesel engine. When there is a difference between the target EGR rate and the estimated EGR rate, the target MFB50 can be modified. When the EGR correction with closed-loop control was applied to engine control, the emission peak in the transient state was mitigated. In particular, the NOx emission decreased by up to 30 % compared to the emissions without the EGR estimation model.