The invention belongs to the technical field of X-ray pulsar autonomous navigation and discloses an X-ray pulsar navigation TOA estimation method based on Bayes estimation. Under the condition that the overall trend of a photon counting rate accords with the Poisson distribution, an X-ray photon arrival time sequence can be modeled into a non-homogeneous Poisson process; the flow characteristics of PSR B0531 + 21 pulsars accord with the Poisson distribution, and a Poisson distribution signal model is established and divided into a time-frequency model and a frequency-stabilizing model; the frequency-stabilizing model of the photon sequence is selected to perform Fourier transform and then the frequency-stabilizing model is converted into a frequency domain to obtain a photon flow probability function expression with time delay estimation parameters; the photon flow probability function expression is converted into a likelihood function capable of calculating a time delay parameter by using a Bayes theorem for solving; and a Tool multi-mode nested sampling algorithm is calculated by Bayes estimation, iteration is carried out, and the parameter estimation value of the likelihood function is further calculated. The invention effectively improves the TOA estimation precision within the observation time and meets the future engineering development requirement of pulsar navigation.