Habitat suitability index (HSI) has been widely used in fishery resources exploitation, management, assessment and protection since it was found in the early 1980s, and it has become one of the most important tools in fishery science research. In this article, outlining the studies in the world, the theory and methods of HSI, and the advance applications and exist problems have been summarized. Some advice should be considered sufficiently in the application of HSI, i.e., (1) study on target species’ life history and biological characteristics and its habitats; (2) suitable environment factors should be selected according to different growth stages; (3) research on spatialtempral scales of data and rule set on data; (4) selecting logical weights upon different factors based on literature and expert knowledge; (5) selecting preparatory HSI models be propitious to the various goals, such as protection area, fishing ground and biomass evaluation; (6) selecting suitable HSI models by comparison of models and related analysis; (7) modifying models using insitu or recent data in order to improve precision of model.