To accurately and efficiently calculate the frequency response of the lumped parameter equivalent circuit model (LPECM) of a transformer winding is the basis for studying the simulation method of the frequency response analysis (FRA). In this paper, two different cut-set matrix (CSM) methods, including fundamental cut-set (FCS) and independent cut-set (ICS) matrix methods, are proposed to calculate the FRA curves of the LPECM of a three-winding power transformer. First, based on graph theory and electrical circuit laws, the basic CSM equation is deduced. Second, four different FCS matrix selection methods of the LPECM are introduced and the best FCS matrix is determined by deeply analyzing their characteristics. Then, an ICS matrix method is proposed to obtain the ICS of the LPECM. Furthermore, FCS and ICS are taken into the CSM equation to calculate the FRA results of the LPECM, respectively. Finally, the accuracy of the proposed methods is validated by Multisim software and the performance of these two methods is compared with node voltage matrix (NVM) method by analyzing the calculation time. The results show that FCS and ICS matrix methods both can be used to accurately obtain the FRA results of the LPECM of the three-winding power transformer, but ICS is more simple than FCS matrix method due to avoiding the procedure for the selection of the tree. In addition, since ICS matrix method has the shortest running time among these methods, it can be used to improve the calculation efficiency of the FRA curves of the LPECM of a three-winding power transformer.