The optimization of the inter-satellite link assignment is an important technical issue,especially,for the case that the number of inter-satellite spot-beam antennas is less than assignable links.Based on Minimum Spanning Tree(MST) theory in graph theory,this paper proposes a link assignment algorithm for the hybrid navigation constellation using GEO,IGSO and MEO satellites.Using GEO satellites as the core transfer node,this algorithm assigns inter-satellite links with lower communication costs firstly,and then assigns links at least once for all visible satellites by applying the iterative assignment.As a consequence,the integrated optimization of the inter-satellite observing and communication performance can be achieved.The simulated results show that,compared to the mesh-link assignment algorithm used for the Iridium system,the proposed link assignment algorithm can be able to improve the precision of orbit determination and reduce whole-network average communication delay.