Sea cucumber (Apostichopus japonicus) is an important economic species in the Bohai and Yellow Seas of China. In recent years, due to anthropogenic factors, the marine environment has undergone dramatic changes, and the wild sea cucumber resources are facing a crisis. Restoration of sea cucumber populations and development of artificial aquaculture facilities would require assessment of the suitability of their habitats. Principles of ecological dynamics, physiological characteristics and behavioral habits of sea cucumbers are used in this study to select key habitat factors related to the growth of sea cucumbers. Two-dimensional hydrodynamic model of the Bohai and Yellow Seas and ecological growth model for sea cucumbers are used to develop a habitat suitability index (HSI) model for sea cucumbers. A new habitat factor, water flow velocity, was incorporated. A combination of subjective and objective weighting methods were used to make the sea cucumber habitat suitability assessment more comprehensive and objective. This new model was used to assess the habitat suitability of sea cucumbers in the Bohai Sea and the northern Yellow Sea, providing theoretical support for habitat restoration and fishery production.