Honda developed a new generation 1.6L diesel engine as a part of technologies for high driving performance and good fuel economy. This new engine is equipped on Civic (C Segment, 5 doors), launched as a new European model in 2013. This engine has some technologies achieving both good fuel economy and low emission, and met Euro5 emission regulation. And the Civic achieved CO2emission of 94 g/km in NEDC, a reduction of 14.5% in CO2 emission against the previous diesel engine of Honda. This engine has the dual EGR system composed of HP-EGR and LP-EGR, one of the technologies introduced to increase fuel efficiency. In this paper, some issues for the dual EGR system control and countermeasures for them will be described.In order to control each EGR mass flow, two or more valves (HP-EGR valve, LP-EGR valve and intake throttle) should be regulated cooperatively. So the model based control which is multi input-multi output (MIMO) system is introduced, and operates some valves simultaneously. In the dual EGR system, the ratio of LP-EGR flow and HP-EGR flow should be controlled. So the logic which guarantees minimum differential pressure to LP-EGR was introduced. And then LP-EGR flow indicates lag and dead-time characteristics because LP-EGR passage is very long. In this case HP-EGR which has higher response is compensated, and achieves accurate EGR control. This model based control is used in the rich combustion mode also in order to realize the cooperative control of an intake shutter and HP-EGR valve. Introducing the model based control realizes good control accuracy of EGR flow regardless of the dual EGR using some valves.