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Advanced oxidation process (AOP), with a high oxidation efficiency, fast reaction speed (relatively no secondary pollution), has become one of the core technologies of industrial wastewater and advanced drinking water treatment. Heterogeneous Fenton-like oxidation process (HFOP) is a kind of AOP, which developed rapidly in recent years in such a way to overcome the disadvantages of traditional Fenton reaction. Metal-organic frameworks (MOFs) and their derivatives become essential heterogeneous catalysts for organics mineralization due to the large specific surface area, abundant active sites, and ease of structural regulation. However, the knowledge gap on the mechanism and the fate of heterogeneous catalyst species during organics degradation activities by MOFs presents considerable impediments, particularly for a wide application and scaling up the process. This work has the potential to provide guidance and ideas for researchers and engineers in the fields of environmental remediation, environmental catalysis and functional materials. This review focuses on clarifying the critical mechanism of •OH production from MOFs and derivatives as well as its action on the organic’s degradation process. The recent developments in MOF based HFOP are compared, and more attention is paid for the following aspects in this review: (1) classifies systematically progressive modification methods of MOFs by chemical and physical treatments; (2) analyzes the fate of catalytic species during treating organic wastewater; (3) proposes design ideas and principles for improving the performance of MOFs catalysts; (4) discusses the main factors influencing the catalytic properties and practical application; (5) summarizes the possible research challenges and directions for MOFs and their derivatives as catalysts applied to wastewater treatment in the future.