When the OFDM system uses the RootMUSIC algorithm to complete the joint TOA and DOA estimation, the required roots appeared in the form of conjugating symmetry which will be computational redundancy. Aiming at this problem, a RootMUSIC algorithm based on spectral factorization—SFRootMUSIC algorithm is proposed. Based on the structural characteristics of Laurent polynomials, the algorithm uses spectral decomposition to reduce the order for the root polynomial by a half, which reduces the computational complexity, completes independent delay and angle estimation, and constructs a cost function of parameter pairing, complete the joint estimation. The simulation results show that the SFRootMUSIC algorithm has similar estimation performance with the RootMUSIC algorithm, and its complexity is lower. When the number of array elements is 12,the number of subcarriers is 512 and the number of snapshots is 512, the complexity can be reduced by 6994%. The proposed algorithm can achieve the joint estimation of TOA and DOA with lower complexity while ensuring the accuracy, which verifies the proposed algorithm is more suitable for realtime computing.