The invention discloses a three-way static stiffness test system of a machining center. The system comprises a false cutter for applying a load, a data acquisition and processing system, and a three-way load applying device and a sensor adjusting and fixing device which are connected with the data acquisition and processing system. The data acquisition and processing system comprises a data acquisition device connected with a pressure sensor and an eddy current displacement sensor, and a computer. The three-way load applying device comprises a fine tuning platform for three-dimensional spatial direction adjustment and a top element arranged on the fine tuning platform. The sensor adjusting and fixing device comprises a bracket which is connected with a screw lift. The eddy current displacement sensor is arranged above the screw of the screw lift. A test method of the test system is also disclosed. The three-way static stiffness test system and method of a machining center can efficiently test the static stiffness of a machine tool in the XYZ directions in a three-dimensional space, ensure that the direction of acting force is consistent with that of the measured static stiffness, and has high precision.