The invention relates to a waveform design for a formation flying satellites SAR (synthetic aperture radar), and provides an orthogonal waveform designing method which is used for carrying out phase encoding for linear frequency modulation (LFM) signals. The orthogonal waveform designing method includes generating a linear frequency modulation signal at first, dividing the linear frequency modulation signal into N parts according to equal time intervals to form N sub-pulses, carrying out random phase encoding for each sub-pulse by M times according to the number M of the formation flying satellites, establishing an ambiguity function expression, calculating cluster tolerance xi meeting formation flying satellite synthetic aperture radar Doppler mismatch, finding out a critical N value meeting requirements by the aid of a searching comparison method, finally selecting energy and functions which are in autocorrelation and cross-correlation as cost functions, namely fitness functions in genetic algorithm, searching code values of phase encoding of the various sub-pulses by the aid of the genetic algorithm, and finding out orthogonal waveforms after optimization at last. The waveforms have low autocorrelation side lobes, cross-correlation peak values, bandwidth occupation ratio and Doppler mismatch, and excellently suppress echo signal interferences among different space-borne SARs.