The invention discloses a submerging type ecological water cube system used for black and stink water body pollution treatment, ecological restoration, water quality improvement, and water body maintenance in rivers, lakes, reservoirs, river mouths, and gulfs. The submerging type ecological water cube system comprises tank bodies, aeration guide rods, ecological water lungs, emergent aquatic plants, submerged plants, a microbial carrier inoculated with microbes, and external artificial light sources; the emergent aquatic plants and the submerged plants grow on system upper surface and peripheral side surfaces respectively, so that full utilization of the three-dimensional space from water bottom to water surface is realized, the contact effect area of plants with water body is enlarged, full absorption on nitrogen phosphor, reduction of suspension matters, and supplement of ecological oxygen demands are realized; the microbial carrier is inoculated with a microbial agent to increasedmicrobe contact effect specific surface area; the ecological water lungs composed of aquatic animals are used for filtering and eating of eutrophic substances such as planktonic algae, suspension particles, and organic chips, water plant photosynthesis and adsorption effect on nitrogen and phosphor are promoted, water body black color and stink smell are eliminated, and a water body ecological system is established.