A novel prediction method for robust beating heart tracking is proposed. The dual time-varying Fourier series is used to model the heart motion. The frequency parameters and Fourier coefficients in the model are estimated respectively by using a dual Kalman filter scheme. The instantaneous frequencies of breathing and heartbeat motion are measured online from the 3D trajectory of the point of interest using an orthogonal decomposition algorithm. The proposed method is evaluated based on both the simulated signals and the real motion signals, which are measured from the videos recorded using the da Vinci surgical system.