To ensure the safety and the production efficiency as well as the component lifetime of deep-sea mining system, a novel heave compensation system of deep-sea mining based on dynamic vibration absorber was proposed in the light of 5000m deep sea poly-metallic mining system of China in this paper. According to the work condition of heave compensation system, the response of deep-sea mining ship under random wave of sea state 4 in China’s deep sea poly-metallic mining field are numerically simulated in time domain. The proposed heave compensation system was simplified to a two-degree-of-freedom system stimulated by the displacement motion of the deep-sea mining ship and its dynamic model was built. Taking the minimum of the displacement variance of the proposed heave compensation system as the optimal object and considering the allowed displacement of the dynamic vibration absorber itself, the computation formula of the optimum parameters of dynamic vibration absorber for heave compensation system of deep-sea mining is derived. Thus the parameter of dynamic vibration absorber was determined and its effect on the performance index of the heave compensation system was simulated and compared. The dynamic vibration absorber with optimum parameters was simulated and tested on the test bench of double-storey mass-spring vibration system in the lab. The results of the example show that the performance of vibration control of the designed dynamic vibration absorber is satisfactory and the computational formulas given in the paper are effective. The results also verified that the heave compensator based on dynamic vibration absorber with the optimal parameters can have good performance of heave compensation and it is practical to isolate the lifting pipeline and its deployment platform from the vibration of the ship motion induced by the irregular wave with simplicity and less energy consumption. This work in the paper will be of great theoretical guidance in the optimum design of the dynamic vibration absorber for heave compensation system of deep-sea mining.