The invention discloses a test system for the water tightness test of a tunnel deformation joint waterstop, which comprises two steel tanks mounted, in a sealed manner, at two sides of a waterstop to be tested, a steel structured test bench, an atmospheric pressure test bench, a hydraulic pressure test bench, an air compressor, a remote-distance full-automatic observing and reading apparatus and a safety protection device. The test device of the invention can be used for the water tightness test of a plurality of waterstops, realize random opening displacement and shear displacement accurately, and simulate the stress condition of deformation joint waterstop structure under different working conditions by applying atmospheric pressure in balloon to a tested object through the atmospheric pressure test bench and applying hydraulic pressure to the steel tanks through the hydraulic pressure test bench to simulate seawater pressure. The system and the method are suitable for the test of OMEGA waterstops and GINA waterstops as well as expandable waterstop.