The invention discloses a joint frequency phase estimation method based on partial decoupling. The problem of failed subsequent phase offset estimation caused by large carrier frequency offset of traditional joint frequency phase estimation is solved. The technical scheme comprises the steps that 1 on a receiving end, any pilot signal is demodulated to acquire a demodulated signal; 2 correlation operation is carried out on the demodulated signal and a delayed signal whose sampling time interval is alpha, and the result of the correlation operation is used to acquire a frequency offset estimation value; and 3 the maximum likelihood phase offset estimation is carried out on the conjugate form of the correlation operation result taking alpha as the half of the pilot length and the demodulatedsignal jointly to acquire a phase offset estimation value. According to the invention, the anti-frequency offset ability of phase offset estimation is improved; the complexity of phase offset estimation is reduced; the sampling zero time position of the receiving end is not manually set; the feasibility in practical applications is improved; and the method can be used for space communication including satellite communication, unmanned aerial vehicle communication and spaceflight test control.