Molybdenum-based electrocatalysts have been widely applied in electrochemical energy conversion reactions. The essential roles of defects, including doping, vacancies, grain boundaries, and dislocations in improving various electrocatalytic performances have been reported. This review describes the latest development of defect engineering in molybdenum-based materials for hydrogen evolution, oxygen reduction, oxygen evolution, and nitrogen reduction reactions. The types of defects, preparation methods, characterization techniques, and applications of molybdenum-based defect materials are elucidated. Finally, challenges and future research directions for these types of materials are also discussed.