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The theory of the term structure of interest rates is of fundamental importance in financial engineering. In this paper, Square-Root Unscented Kalman Filter (SRUKF) algorithm is used to estimate a popular term structure model of interest rates. Simulation tests are conducted based on SRUKF and Extended Kalman Filter (EKF) respectively. The numerical results show that both approaches are capable of tracking changes in term structure and demonstrate the superior performance of SRUKF-based estimator.