In order to enhance the accuracy of the relative velocity measurement for the Mars explorer formation flight, we develop a relative velocity measurement method. In this method, the spectrometers at two Mars explorers are adopted to measure the starlight frequency shift and to estimate the velocity with respect to the star. Unfortunately, the instantaneous velocity of star can not be predicted accurately, which results in a large error in the velocity measurement. The difference of these two velocities, which does not include the proper motion of star, is the relative velocity between a pair of Mars explorers at the direction of the star. However, this navigation method can not work alone because of unobservability. To make the navigation system observable and improve the accuracy of both absolute and relative navigation for the Mars explorer formation flight, we combine it with X-ray pulsar navigation and the inter-satellite links, and propose an autonomous integrated navigation method with observability. In this integrated navigation scheme, the extended Kalman filter is adopted to deal with the relative velocity, the inter-satellite links and the pulse time-of-arrival, and estimate the absolute and relative navigation information for the Mars explorer formation flight. The simulation results demonstrate that both absolute and relative navigation accuracy of the proposed method are higher than that of the pulsar navigation, especially the relative one.