The invention provides an experimental device for an in-situ research of an ecological niche of seawater micro-plastic and an application method, and belongs to the field of marine environments. The experimental device comprises an anchoring system, a bearing system, a ballasting system and a collection system, wherein the anchoring system is connected with the bearing system; the ballasting system is connected above the bearing system; the collection system is used for collecting an obtained sample. According to the experimental device provided by the invention, experimental conditions consistent to environment parameters including natural seawater water temperature, salinity, pH (Potential of Hydrogen), nutrient salt and the like are created to carry out an in-situ experiment; the disadvantages of uncertainty and complexity of investigating and collecting materials, shapes and sizes of the micro-plastic on the scene, and difficulty in recovering a real marine environment under laboratory conditions are overcome. Meanwhile, the ballasting system in the device realizes automatic upward floating and sinking of the bearing system, and a sample is convenient to feed and collect. Furthermore, the collection system has good shipboard operation coordination performance and is rapid in collection; the application of the device provided by the invention provides important guarantees for analyzing structure characteristics of the ecological niche of the micro-plastic and correlation with environment factors.