The invention discloses a flexible pedestal testing system of a launch canister. The system comprises an upper cover plate assembly, an initial chamber, a flexible pedestal, a lifting gear and landing legs. The initial chamber comprises fixed walls for forming side walls of the initial chamber and a movable wall. An opening positioned at one side of the movable wall on the initial chamber is sealed through the flexible pedestal, and an opening at the other side of the movable wall is sealed through a fixed cover plate. The fixed walls are fixedly connected on an upper cover plate assembly. The landing legs are fixed on the upper cover plate assembly. The system also comprises an air inlet arranged on the initial chamber, a pressure device which is sealingly connected with the air inlet and can make pressure in the initial chamber reach required pressure, an exhaust vent which is arranged on the initial chamber and is sealingly connected with an exhaust vent cover, and a control device for opening or closing the exhaust vent cover. By the adoption of the flexible pedestal testing system of the launch canister, a water pressure static load test can be carried out on the flexible pedestal, and a dynamic load test also can be carried out. Test types of the flexible pedestal testing system of the launch canister are increased, and then practicality of the flexible pedestal testing system of the launch canister is enhanced.