A method to calibrate the transform matrix between the sun sensor coordinate system and the cubic prism coordinate system was proposed.Firstly,the sun sensor coordinate system and a 2D rotator coordinate system were calibrated with a sun simulator and a high-accuracy 2D rotator.Then,the cubic prism coordinate system and the 2D rotator coordinate system were calibrated with a diaphragm screen and a CCD image-collimate system.Finally,the transform matrix between the sun sensor coordinate system and the cubic prism coordinate system was derived by taking the 2D rotator as a medial coordinate system.Thereby,the sun vector measured by the sun sensor was indirectly transferred to the cubic prism coordinate system.Experiment results show that the calibration precision is better than 4″(1σ) ,which can meet the requirement of sun sensor measurements.Proposed method can relax the demands for precise machining and installation,and the sun sensor and 2D rotator coordinate systems shouldn't be in coincidence when calibration.It shows that the method is easy to carry out and worth to use.