Full Polarization Interferometric Radiometer (FPIR) is a one-dimensional full polarization Interferometric radiometer for the Sea Surface Salinity (SSS). A ground-based prototype has been developed to demonstrate the concept and performance of the instrument. To achieve the SSS measurement accuracy, a new calibration system has been designed for FPIR. And a new calibration procedure has been developed to improve the instrument performance. In this paper, the calibration system and the new calibration procedure for FPIR are designed and evaluated by the FPIR ground based prototype.