We theoretically explain how to achive the quantum coherent control of multi-photon transition by phase-modulated lightfield. The interaction between several types of shaped laser pulse and a two-level system is studied within the weak field regime. Quantum diffraction effect during the two-photon transition affected by a shaped laser pulse is studied. Under the perturbation theory, the analytical solutions of multi-photon transition probabilities are obtained. Based on these analytical expressions, we demonstrate that the quantum coherent control of multi-photon transition is affected by step-phase modulated laser and cosinusoidally phase modulated laser. It is shown that the elimination of transition probabilities exist in these two processes, and the two results have different probability elimination positions.