Global marine fishery resources have shown a remarkable declining trend due to overfishing, climate change, environmental pollution and habitat destruction in recent decades. As a promising solution to the current challenge, fisheries stock enhancement is believed to be an important way to restore resources and maintain sustainable development of fisheries. At present, many countries in the world, including China, have carried out diverse enhancement programs on varying temporal and spatial scales, including a large body of juvenile releasing. Meanwhile, studies also have pointed out that many stock enhancements failed to achieve the expected goals while some even led to negative ecological impacts, which sounded a remarkable warning for the future development of enhancement. This study briefly reviewed the progress of fishery stock enhancement in China and abroad, mainly focusing on the scientific problems about the assessment of stock enhancement. We firstly examined the research topics on stocking strategies, including the choice of releasing time and locations, size of juveniles, releasing tactics, juvenile density, genetic effects and their interactions. We then reviewed the methods commonly used in the assessment of stocking effects and the ecological impacts from the ecosystem perspective, and summarized the methods into four categories, that is, assessment models based on mark-recapture, YPR model, population dynamics model and ecosystem model, respectively. Based on the understanding of the complexity of stock enhancement system, we demonstrated the key ecological processes, ecological mechanism and spatial-temporal scales in the processes of enhancement. We further discussed the direction of methodological development for stock enhancement evaluation, and advocated that fundamental principles, ecological effects, and spatial structure should be increasingly incorporated into the development of assessment models. This article indicates that stock enhancement ecosystems have complex structure and dynamics, and stock enhancement should be planned on the basis of a comprehensive ecosystem understanding. Prospective assessment research should be developed to support stock enhancement planning and risk avoidance. This study may provide scientific references for the research and practices of stock enhancement by exploring the shortcomings and development of fisheries enhancement evaluation.