A full-cycle three-dimensional computational fluid dynamics (CFD) model coupled with detailed chemical kinetics has been developed to investigate the effect of late intake valve closing (IVC) on combustion and emission characteristics in a diesel engine with premixed charge compression ignition (PCCI) combustion. The application of late IVC was demonstrated to provide efficient control of ignition timing and significant reduction of nitrogen oxides (NOx) and soot emissions by decreasing the effective compression ratio and increasing premixing, but it possibly led to increases of hydrocarbon (HC) and carbon monoxide (CO) emissions due to low combustion temperature and insufficient oxygen amount. Parametric studies by varying intake pressure, exhaust gas recirculation (EGR) rate and start of injection (SOI) timing with varied IVC timing were conducted to explore the potential of late IVC for emission reduction in diesel PCCI engines. The results showed that, with assistance of increasing intake pressure, late IVC could reduce NOx, soot, HC, and CO emissions simultaneously. A certain EGR rate and optimized SOI timing were always necessary to maintain satisfactory NOx and soot emissions for diesel PCCI combustion.