Abstract: The space search method of X-ray Pulsar Navigation(XPNAV) system ambiguity resolution tests all the vectors in the space,which results in its high complex computation.A new XPNAV system ambiguity resolution algorithm was presented,which limited the correct ambiguity vector to subspaces according to pulsar characteristic period and found the seed vectors of the subspaces using linear search method.Then,the subspace was traversed using exhaustive algorithm based on full binary tree,and the relation among the ambiguity vectors in the subspace was set up simultaneously.Theoretical analysis and experimental simulation show that the new method can reduce the complexity of computation significantly,and due to the constant matrixes depend on pulsar attribute parameters,it is easy to implement in engineering.Besides,the binary tree based search method can also be of parallel implementation.