This paper investigated the effects of late intake valve closing timing (IVCT) and two-stage turbocharger systems matching based on partially premixed combustion strategy. Tests were performed on a 12-liter L6 heavy-duty engine at loads up to 10 bar BMEP at various speed. IVCT (where IVCT is -80°ATDC, -65°ATDC and -55°ATDC at 1300 rpm, 1600 rpm and 1900 rpm, respectively) lowered the intake and exhaust difference pressure, reducing pumping loss and improved the effective thermal efficiency by 1%, 1.5% and 2% at BMEP of 5 bar at 1300 rpm, 1600 rpm and 1900 rpm. For certain injection timings and EGR rate, it is found that a significant reduction in soot (above 30%) and NOx (above 70%) emissions by means of IVCT. This is due to that IVCT lowered effective compression ratio and temperature during the compression stroke, resulting in a longer ignition delay as the fuel mixed more homogeneous with the charge air ahead of ignition. At 1300 rpm, 10 bar BMEP, the effective thermal efficiency is slightly decreased by means of IVCT. However, at 1600 rpm, 1900 rpm 10 bar BMEP, the effective thermal efficiency is increased by employing IVCT. It is also owing to that the reduction of the pumping work. Above all, IVCT played an important role to make homogeneous distribution of the equivalence ratio Φ and reduced the pumping loss due to decrease in pressure difference of intake and exhaust.