The invention discloses a radar orthogonal waveform design method based on frequency modulation and phase modulation of a chaotic sequence, comprising the following steps: S1, using a chaotic system to generate a chaotic sequence of which the length is N*P, and cutting the chaotic sequence into P sequence sections (the length of each sequence section is N), selecting one sequence section, and letting the sequence section be {x(0), x(1), x(2),...,x(N)}; S2, encoding a chaotic joint frequency modulation and phase modulation signal, dividing a pulse into a series of equal sub pulses, and carrying out frequency modulation differently on different sub pulses, and then, using the sequence section obtained in S1 to carry out phase encoding on each cycle of a waveform in each frequency encoding sub pulse, and obtaining a phase-frequency joint modulation chaotic radar signal through use of a randomly-generated initial phase; and S3, calculating a complex envelope signal of the phase-frequency joint modulation chaotic radar signal obtained in S2. The signal frequency and phase change as a chaotic signal changes, the orthogonality of signals is improved, and the interception probability is reduced.