Vessel-borne platforms adjust the position and orientation of their supporting surfaces by means of their actuators to isolate vessel motions from vessel-borne equipment they carry, so as to ensure the vessel-borne equipment operation is like onshore. A three-degree-of-freedom parallel scale vessel-borne platform prototype is designed and constructed, which can operate in the sea state of 2.5m significant wave height. Based on this prototype, a wave compensation rapid control prototyping (RCP) system of the parallel vessel-borne platform is developed using a personal computer (PC) and an OP4510 simulator, as well as MATLAB and RT-LAB software. Taking a joint space wave compensation control scheme as an example, we verify the control scheme by experiment, where this control scheme is realized using MATLAB/Simulink and compiled into an executable file under the Redhat system and downloaded to the OP4510 simulator through RT-LAB. Therein, OP4510 simulator acts as a prototype controller to control the scale vessel-borne stabilization platform prototype. The experimental results verify that the taken joint space wave compensation control scheme could make the vessel-borne platform supporting surface be kept at a desired horizontal orientation, while verifying the effectiveness of the developed wave compensation RCP system. The developed wave compensation RCP system can shorten the development cycle and reduce the development cost of real wave compensation controllers.