Independent and autonomous running of the entire GNSS system in navigation warfare is one of the most important aims of building inter- satellite links. However, it is inevitable that inter-satellite links will be faced with the threats from jams in navigation warfare, which may result in performance declining, or even breaking down. Therefore, exact evaluation of anti-jamming performance is very important. Ant- jamming performance evaluation of inter-satellite links system is much more difficult than other objects, as it is related to almost every aspect of the system, such as the design of signal system, network, linking strategy, equipment performance, and so on. In order to accurately evaluate the anti-interference performance of the entire inter-satellite links network under the conditions of navigation warfare, this study firstly analyzed a variety of factors which affect the anti-jamming performance of inter-satellite links. On this basis, test scenarios for anti-jamming performance evaluation was modeled and designed. And then an evaluation method for anti-jamming performance of inter-satellite links system based on average availability was proposed, and the index system for availability evaluation was defined, which made accurate and quantitative evaluation of anti-jamming performance of the entire inter-satellite links network possible.