In the distributed feedback fiber laser sensor interrogation based on 3×3 coupler, the asymmetry of the 3×3 coupler and the inconsistency of detectors lead to harmonic distortion in the result. This paper presents an improved method that combines the 3×3 coupler and the extended Kalman filter (3×3-EKF method) to effectively suppress the harmonic distortion in real-time. The coefficients of the three ellipses formed by every two-channel interference fringes were estimated using EKF. The system parameters were corrected based on these coefficients to eliminate the dependence on the idealization of 3×3 coupler and detectors. The result shows that the 3×3-EKF method can update the system parameters with a frequency up to 500 kHz. A total harmonic distortion less than 0.1% can be achieved with signal frequency ranging from 20 Hz to 1 kHz. Besides, the system shows a minimum detectable wavelength shift of 3.1 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-7</sup> pm/√Hz @ 1 kHz, and a large dynamic range of 135 dB @ 100 Hz.