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This paper addresses the problem of building the X-ray pulsar timing model that is an essential work for X-ray pulsar navigation(XNAV).We propose a theoretical discussion of the differences between the X-ray and radio pulsar timing and develop a complete processing framework.In this framework,the 2mZ-test method is deduced by the theory of the Fourier Series Estimator(FSE)in the complex form.A fast maximum likelihood(FAML)estimator is applied for the estimation of pulse time of arrival(TOA).Then the model parameters are deduced based on a least-squares strategy.To sustain this framework,about 173 ks observations with X-ray pulsar navigation-I(XPNAV-1)satellite over 30 days are utilized for experimental studies.The results show that the proposed framework is valid,and the phase residuals with the X-ray model parameters is 2.57 milliperiods.