The Atkinson cycle has been studied as one strategy for premixed charge compression ignition (PCCI) combustion that can reduce NOx and soot emissions. A high exhaust gas recirculation (EGR) is employed to reduce the detrimental engine-out emissions from automotive engines, but it deteriorates the fuel economy of vehicles. Not only can the Atkinson cycle achieve simultaneous reduction in particulate matter (PM) and NOx emissions without increasing fuel consumption, but it can also expand the applicable operational range of the PCCI strategy. Late intake valve closing (LIVC) was used to produce the Atkinson cycle in this study, and the emissions and combustion characteristics of a PCCI diesel engine were investigated using a 30 degrees LIVC in combination with various operating parameters, such as EGR rate, injection timing, swirl ratio, and intake pressure. A LIVC strategy with advancing second injection timing leads to a low compression ratio such that it can reduce NOx emission while the PM emission level and break-specific fuel consumption (BSFC) remain constant.