Pulsar navigation is a possible measurement of spacecraft navigation autonomous navigation,and profile folding and measure is one of the core technologies of it,whose performance determines the capability of the final navigation result.Current profile folding measures are commonly based on the presumption that the time of photon arrival can be transformed to the solar system barycentreand the presumption that folding profile is exactitude.However,on the real navigation scene,since the position and the velocity of the spacecraft are not exactly acquirable,folding profile would bring deformation and therefore cause the phase measure error.In order to solve this problem,this paper introduces the loop tracking to the pulsar navigation profile folding and measurement processing.By lock the difference between measure phase and predict phase,the period feedback can be realized to rise the accuracy of the pulsar phase measurement.The result shows that this method could improve the profile folding and phase measure result,and suits for dynamic pulsar navigation.