The accurate measurements for fiber propagation delay is the prerequisite of timing accuracy in high precision optical fiber timing system. A certain of processing is needed for measurements because the original measurements generally cannot meet the accuracy requirement. The commonly used methods such as Adjacent-averaging method and modeling method based on the measurement have low efficiency or poor operation in practice. In this paper, the principle of fiber timing and propagation delay measurement are introduced, the latter is the key issue in fiber timing, the characteristics of propagation delay measurements are described from a simplified fiber timing system, which is based on the two-way optical time transfer (TWOTT), and the separate effect of the characteristic is analyzed for timing accuracy. On the basis of the characteristics of propagation delay measurements, the improved strategies are defined based on Kalman filter theory. Finally, the effectiveness of the modified Kalman filter is validated through simulation study.