This paper presented a new orthogonal polyphase signal design method based on the ambiguity and cross ambiguity function of polyphase codes to design orthogonal polyphase sequences with a very low aperiodic autocorrelation peak sidelobe level (PSL), low aperiodic cross-correlation and a good tolerance to Doppler shifts for orthogonal multiple input multiple output (MIMO) radar. An efficient Genetic Algorithm (GA) is used to numerically optimize such orthogonal code sets. Some of the designed new polyphase sequence sets are presented with good correlation properties as well as resilience to Doppler shift. The simulation results and comparisons with the existing sequences show that the proposed algorithm and criterion are effective for the design of polyphase sequences with superior aperiodic correlation and Doppler properties.