The invention belongs to the fields of water conservancy engineering, buildings, bridges, sea bank revetments, and the like, and particularly relates to a nano modified cement-based underwater non-dispersible material and a preparation method thereof. The material is prepared from cement, mineral powder, silica fume, a superplasticizer, a defoamer and other materials, a certain amount of nano-SiO2or CaCO3 and a preferred flocculant are added, the materials are mixed evenly through a mixer, and then quartz sand is added to obtain the nano modified cement-based non-dispersible material. According to the nano modified cement-based underwater non-dispersible material, the fluidity reaches 260 cm, the underwater self-leveling can be realized, good dispersion resistance is achieved while high fluidity is achieved, the content of suspended matter is lower than 80 mg/L, 1d strength is nearly 20 MPa, and 28 d strength is greater than 50 MPa, and the micro expansion effect is achieved. The nanomodified cement-based underwater non-dispersible material can be in the forms of dry powder, wet mixed mortar or concrete, and the like, can be made into dry powder materials, and can be directly used for underwater construction by being mixed with water added on site, large-scale production and application are achieved easily, and the application requirements of the fields of the water conservancy engineering, the buildings, the bridges, the sea bank revetments can be met.