In diesel engines, valve avoiding pit (VAP) is often designed on the top of the piston in order to avoid the interference between the valves and the piston during the engine operation. With the continued application of the downsized or high power density diesel engines, the depth of VAP has to be further deepened due to increased valve lift for more air flow into and out of the cylinder and decreased piston top clearance for less HC/CO and soot emissions. The more and more deepening of VAP changes the combustion chamber geometry, the top clearance height and the injector relative position to the piston crown. In this paper, a 3-D in-cylinder combustion model was used for a heavy duty diesel engine to investigate the effects of the depth of VAP on combustion process and emissions. Five depths of VAP were designed in this study. In order to eliminate the influence of compression ratio, the piston clearance height was adjusted for each VAP depth to keep the same compression ratio. Subsequently, injector position was adjusted in two ways, to keep the same protrusion height (Case1) or to keep a constant distance (Case 2) between the injector and the piston crown. The simulation results show that, when VAP is less than 4mm, its influence on combustion is less noticeable, with a drop of IMEP less than 0.9%. However when VAP is greater than 4mm, it leads to an evident drop of IMEP. It is also found that the deepening of VAP is beneficial for reducing soot and NO emissions. On the other hand, effects of the two Cases on IMEP are almost the same, but Case 2 leads to much lower cylinder pressure and temperature and longer combustion duration compared to Case 1.