The atomic gravimeter offers high precision, no drift, and excellent long-term stability, making it suitable for high-precision marine gravity measurements. However, the vibration environment generates various noise signals in the shipborne absolute gravity data, compromising measurement accuracy. Specifically, the vibration noise of the Raman mirror significantly impacts the gravimeter's accuracy, necessitating vibration compensation. This article presents an innovative four-coefficient transfer function model for the vibration compensation for a self-designed shipborne absolute gravity measurement system. Then, the particle swarm organization is introduced to identify the optimal compensation coefficients. Testing of the shipborne atomic gravimeter in the mooring state demonstrated an 81.25% reduction of the standard deviation of residuals (σ) between atomic interference fringes and the iterative fitting curve after compensation, yielding a measurement standard deviation of 0.210 mGal. This method was also applied to the test in the sailing state, achieving a 57.97% reduction of σ, with the external coincidence accuracy of 0.407 mGal.