During the transmission process of time synchronization signal in troposcatter channel, the multipath effect and noise of the channel can contribute jitter to time synchronization signal. In order to mitigate this jitter, the EMD (empirical mode decomposition) combined with wavelet threshold model was proposed. In the combined model, the EMD was used to decompose the original signal, the wavelet threshold was adopted to process the decomposed components and then the processed results were utilized to reconstruct the final signal. In order to improve the jitter mitigation effect and the signal authenticity of the combined model, the traditional threshold function in wavelet threshold was perfected by the better coherent and gentler threshold function. Experimental data were used to demonstrate this combined model. Compared with the simplex model and the Kalman model, the combined model has advantage in effect of de-noising as well as authenticity.