Abstract: Sea cucumber (Apostichopus japonicus) is an important economic species in the Bohai and Yellow Seas in 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. The restoration of sea cucumber populations and the development of artificial aquaculture require an assessment of the suitability of their habitats. Based on the principles of ecological dynamics, and after investigating the physiological characteristics and behavioral habits of sea cucumbers, this study selected key habitat factors related to the growth of sea cucumbers. By establishing a two-dimensional hydrodynamic model of the Bohai and Yellow Seas and an ecological growth model for sea cucumbers, a Habitat Suitability Index (HSI) model for sea cucumbers was developed. A new habitat factor for sea cucumbers—water flow velocity—was incorporated, and a combination of subjective and objective weighting methods was used to make the habitat suitability assessment more comprehensive and objective. This model was used to assess the habitat suitability of sea cucumbers in the Bohai Sea and the northern Yellow Sea, providing a scientific basis and theoretical support for habitat restoration and fishery production.