In low-power and high-density real time locating systems, time difference of arrival (TDOA) technique outperforms other ranging techniques. The realization of TDOA-based high resolution indoor localization directly depends on the performance of clock synchronization. In this paper, we introduce a clock synchronization method based on the Kalman filter. The updated clock skew from the Kalman filter is incorporated into the calibration of the difference of arrival time to achieve highly accurate localization of moving targets. Experiments show that our method provides a nanosecond level synchronization resolution and has good robustness to clock synchronization period and non-line-of-sight error, which is quite suitable for indoor localization scenario.