In diesel engines valve avoiding pits (VAP) are often designed on the top of the piston in order to avoid the interference between the valve and the piston during the engine operation. With the continued application of the downsized or high power density diesel engines, the depth of VAPs is further increased. The more and more deepening of the VAPs changes the combustion chamber geometry, the top clearance height and the impingement point of fuel spray. As a result, combustion process and emissions will be impacted due to the variation of squish and swirl flow pattern and air-fuel mixture process. In this paper, a 3-D in-cylinder combustion model based on FIRE software was established for a heavy duty diesel engine in order to investigate the effects of the depth of VAPs on the combustion process. Five different depths of VAP were designed. The piston clearance height was adjusted for each VAP case to keep the same compression ratio. The injector position was adjusted in two ways: to keep the same protrusion height or to keep a constant distance between the injector and the piston crown. The simulation results show that when the depth of the VAP is less than 4mm, their influences on air-fuel mixing and combustion process are less noticeable. When the depth of the VAP is greater than 4mm, however, the fuel spray angle and the turbulent kinetic energy were significantly impacted. This leads to a retard in the phase of 50% of the accumulated heat release, an increase of combustion duration and a drop of indicates mean effective pressure (IMEP). In addition, the study also presents that with the deepening of the VAP, the soot emissions increases in the middle stage of the combustion process, but decreases rapidly in the last stage of combustion process.