The water entry of two-dimensional body with flow separation is simulated based on potential theory and boundary element method. The double point model and four-order Runge-Kutta method and jet-cut model and free surface smooth technique and regrinding technique are used to assure the stability and accuracy of the numerical result. A flow separation model is introduced to simulate the water entry of two-dimensional body with knuckle. The free surface elevation and pressure distribution of wedge with knuckle are predicted and compared with other theory result. Good agreement between numerical result and other theory result is indicated that the numerical method is stability and effective.