X-ray pulsar-based navigation is a novel astronomical autonomous navigation method based on X-ray pulsar observation., The dynamic data processing is one of the key technologies for X-ray Pulsar-based navigation. Especially data processing under the condition of low-orbit and high-dynamic is more difficult than that under the conditions of high-orbit and lowdynamic. Aiming at the measured data with low signal-to-noise ratio,a target function re-estimation method is proposed for the condition of low-orbit and high-dynamic. Furthermore, the principle of the method is analyzed and the mathematical model is constructed. The performance of the method is verified by the measured data from HXMT and XPNAV-1 satellites.