The orthogonal design and multi-factor analysis of variance is adopted to analyze the relationship between macroparameters and microparameters of flat-jointed bonded-particle material and to establish the calibration method of microparameters. Firstly, the orthogonal design is adopted to conduct the macroparameters of flat-jointed contact model and the uniaxial compression, direct tension and biaxial compression numerical test is used to calculate the macroparameters of rock. Then multi-factor analysis of variance and regression analysis are adopted to analyze the relationship between macroparameters and microparameters. On this basis, calibration method of microparameters for rock is proposed in this paper. Based on laboratory tests of limestone, the microparameters of limestone are calibrated. The simulation results are closed to the laboratory test results, and this validated the significance of the proposed method.