Even if the trajectory, rocket shape, bubble generation, development, retro-reflection and collapse in the scaled test satisfy the similarity law, the structural dynamic characteristics are hardly similar, thus, the prototype's load can not be calculated from the test data easily and directly. In this paper, a modified method to calculate the lateral dynamic response of submarine launched missile prototype from the pressure data of scaled model test was presented. The test data was divided into two parts in the method. The first one was related to the bubble retro-reflection and collapse, and the other to the missile body structure vibration. The dynamic response of the prototype was calculated on the basis of the modified method by building mathematical model of the first part of hydrodynamic pressure and expressing the second by added mass and added damping. The modified method and the direct transform method were compared. The results show that their difference can not be ignored. It provided a beneficial reference for load calculation of submarine launched missile.