Due to the tonic and nutritive virtues of sea cucumbers, increased commercial aquaculture has resulted in the expansion of breeding ponds, a primary form of sea cucumber production. Expansion of such production methods has led to increased settling of organic wastes onto the seabed, resulting in enriched sediments. Nitzschia sp. serves as an edible sea cucumber feed. Release characteristics of nitrogen (N) and phosphorus (P) from sediments in the presence of different biomass densities of Nitzschia sp. were studied via laboratory static cultures. pH and dissolved oxygen (DO) in the overlying water and biochemical components (i.e., protein, chlorophyll a) of Nitzschia sp. were assessed. When the biomass of Nitzschia sp. was more than (2–5) × 104 ind/cm2, the release of N and P nutrients was significantly promoted; additionally, the DO content of the overlying water was relatively high and the pH was relatively stable, which favoured the accumulation of proteins and chlorophyll a in Nitzschia sp. The results indicated that Nitzschia sp. promotes the release of N and P in sediments while absorbing them to maintain their own growth and promote the accumulation of nutrients, such as proteins, for the sea cucumbers. At the same time, the algae release oxygen, increasing the DO of the overlying water, providing a healthy breeding environment for the sea cucumbers. Application of Nitzschia sp. has the potential to reduce environmental harm caused by sea cucumber cultivation and thus achieve sustainable aquaculture.