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As the existing MIMO-OFDM synchronization algorithms have the disadvantage of weak practicality and low bandwidth efficiency, a novel synchronization algorithm based on three-dimensional chaotic system is presented in this paper. It constructs the synchronization training sequences using the sequences generated by the three-dimensional chaotic system, and achieves the MIMO-OFDM synchronization using the improved SC algorithm. The likelihood of noise and the sensitivity to the initial values, of which the three-dimensional chaotic sequences possess the nature, improve the security of communication system to some extent. Simulation results show that the algorithm has the higher accuracy of the timing offset estimation and the better performance of frequency offset estimation.