The applications of diesel engines in ground vehicles have attracted much attention over the past decade for the reasons of outstanding fuel economy, power capability, and reliability. With the increasing demand of less greenhouse gas emissions, the current diesel engine fuel efficiency remains unsatisfactory partially due to the conflict between the engine fuel efficiency and engine-out NOx emissions. While advanced aftertreatment systems, such as selective catalytic reduction (SCR) systems or lean NOx trap, have been integrated to diesel engines for reducing the tailpipe NOx emissions, the integrated controls for coordinating diesel engine and SCR system to achieve high engine efficiency and low tailpipe emissions are still limited. The purpose of this study is to develop such an integrated diesel engine and SCR system control method using nonlinear model predictive control (NMPC) approach with both start of injection (SOI) timing and urea solution injection rate as the control inputs. Control-oriented engine models were developed to quantify the influences of SOI timing on engine efficiency and engine-out NOx emissions. Simulation results under US06 driving cycle demonstrate that, given the same catalyst size in total, the proposed controllers are capable of reducing total engine fuel consumption over the driving cycle by 9.36% and 9.50%, respectively, for lumped SCR system and two-cell SCR system, while maintaining high NOx conversion efficiencies and low tailpipe ammonia slip.