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Maritime Autonomous Surface Ships (MASS) are progressing from proof-of-concept to engineering test and initial application phases due to advancements in intelligent sensing, automatic control, and communication technologies. However, numerous studies have shown that the improvement of automation level does not linearly reduce human factor risks. Instead, it exhibits more complex evolutionary characteristics at the medium automation level. In particular, MASS Level 2 (MASS L2) features a “system-dominated, human-supervised” operational mode, and its human factor risks have become one of the key factors restricting the safe operation, large-scale application and sustainable long-term deployment of autonomous ships. This study employs a systematic literature review to analyze 89 core articles (2020–2025) and summarizes the theoretical basis, risk characteristics, and evolutionary trends of human factor risk research in MASS L2. The review results indicate that the current research consensus has gradually shifted from the traditional “human error”-centered explanatory paradigm to a systematic understanding of “information mismatches, opacity, and coupling failures in the human-machine-shore collaborative system”. Typical human factor risks in MASS L2 are mainly manifested as the degradation of supervisory cognition and situation awareness, imbalance in trust in automation, vulnerability in mode switching and takeover, skill degradation, and structural risks in ship-shore collaboration. Based on these findings, this study constructs a classification system and a comprehensive analysis framework for human factor risks in MASS L2, reveals the interaction relationships and dynamic evolution mechanisms among different risk types from a system-level perspective, and further discusses the limitations of existing research in terms of methods, data, and engineering applicability. Finally, considering the development trends of autonomous ship technology, this study proposes future research directions in human factor theoretical modeling, dynamic risk assessment, system design, and operation management. This study aims to provide a systematic knowledge framework for human factor risk research in MASS L2 and offer references for the safety design, safety management, and development of higher-level automation of autonomous ships, while supporting the sustainable and safe advancement of the global intelligent shipping industry.