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In real-time network-based systems with long linear paths, the growth rate of time synchronization error is the major barrier to the scalability of systems even if a transparent clock mechanism of IEEE 1588 is used. This paper is devoted to designing a new time synchronization method for such systems. In the proposed algorithm, a proportional-integral (PI) clock servo is used to achieve the frequency compensation. In order to reduce the growth rate of synchronization error due to the quantization error in timestamping, a Kalman filter is designed based on a state-variable model, which is built for the PI controller-tuned slave clock. In addition, the quantization effect is analyzed and the variance of quantization error is quantitatively estimated for each slave node. Experiments are performed to validate its effectiveness and demonstrate that the peak-to-peak jitter is measured to be only 59.37 ns after four hops, and the growth rate of synchronization error can also be significantly reduced by the presented synchronization method. This indicates that the maximum number of networked nodes can be correspondingly increased.