Water hammer pressure has been known to cause formation fracture and well-control problems. Accurate prediction of water hammer pressure is crucially important to determine the selection of shut-in methods. In this study, the mathematic model of wellbore annulus transient water hammer has been established with the consideration of transient multi-phase flow characteristics, and it has been solved by the Method Of Characteristic (MOC). Finally, this paper focused on the effects of gas cutting, shut-in time and friction on water hammer pressure, and gas kick time were also regarded to study on the influence of water hammer pressure. The results show that both the gas cutting and gas kick time have few influences on the maximum water hammer pressure, but intensified the attenuation of water hammer pressure. Additionally, the peak value of water hammer pressure declines with the increase of the shut-in time, and the effect of friction loss on water hammer pressure became significant with the increase of well depth. More importantly, both the additional water hammer pressure and Shut-In Casing Pressure (SICP) generated by the closure of BlowOut Preventer (BOP) are likely to cause formation at the shallow casing shoe damage.