The second harmonic generation (SHG) produced from two-dimensional atomic crystals have been utilized recently in studying the grain boundaries and electronic structure of such ultra-thin materials. However, the SHG in many of these crystals, such as transition metal dichalcogenides (TMDCs), only occur in odd numbered layers with limited intensity due to their noncentrosymmetric nature. Here, we probe the SHG from the bulk noncentrosymmetric molybdenum disulfide (MoS2). Whereas the commonly studied 2H crystal phase’s anti-parallel nonlinear dipoles in adjacent layers give an oscillatory SH response, the parallel nonlinear dipoles of each atomic layer in the 3R phase constructively interfere to amplify the nonlinear light. Due to this interference, we observed the atomically phase-matched condition yielding a quadratic dependence between the intensity and layer number. Additionally, we probed the layer evolution of the A and B excitonic transitions in 3R-MoS2 using SHG spectroscopy and found distinct electronic structure differences arising from the crystal geometry. These findings demonstrate the dramatic effect of the symmetry and layer stacking of these atomic crystals.