The absolution navigation based on X-ray pulsar is an entirely new autonomous technology. This paper put forward the basic theory of absolution navigation based on pulsar, and proposed a bettered algorithm of integer cycle ambiguity in the method of absolution navigation. Then the algorithm was analyzed deeply and the theoretical derivation was made. Through the simulation solution of ambiguity and position of spacecraft, it can achieve ideal precision. This cycle ambiguity arithmetic provides a new avenue for absolution navigation based on X-ray pulsar.