Maritime Autonomous Surface Ships (MASS) have obtained much attention in recent years. Navigation with human–machine cooperation is the core for L1–L3 MASS. In this article, the development and trend of MASS are collected, and main research institutions are analysed based on MASS experimental projects and publications. The navigation modes of MASS are given, and main topics involved in human–machine cooperative navigation are presented. We focus on the research progress in the four aspects, i.e., modelling of ship navigating behaviour, enhanced navigation situation awareness, human–machine cooperation decision-making and human–machine cooperation navigation control, and then we compare the different methods and technologies for different issues of human–machine cooperative navigation. On the basis of current development, the deficiencies and unsolved problems of MASS human–machine cooperative navigation are analysed. The key theories and technologies of identification and risk assessment of navigating behaviour, situation awareness enhancement, human–machine cooperative decision-making, human–machine cooperative navigation, experimental platform and a case study of human–machine cooperative navigation are investigated, and relevant feasible approaches are provided. We believe the human–machine cooperative navigation will be an important breakthrough of MASS development, and inland and offshore waters will be the suitable navigation area for testing the performance of ship human–machine cooperative navigation.