Doppler frequency shift simulation is a key technique in high dynamic satellite navigation signal simulator. Considering the features of field programmable gate array, a mixed-clk third-order direct digital synthesizer (DDS) simulation model was built, and its output phase expression was derived. The calculation method for initial control word for each stage DDS was given and it was pointed out that the same-clk third-order DDS simulation model is only a special case of mixed-clk simulation model. After analyzing the signal phase error caused by mixed-clk, the word length design method for each stage DDS was discussed. Comparison between the same-clk third-order DDS and the mixed-clk third-order DDS can reduce both resource and power consumption. Simulation results indicate that the proposed method can be used to simulate signal Doppler is of high precision.