The invention provides a method and system for modifying treatment of high-viscosity sea mud. The viscosity of the sea mud can be reduced through three times of dispersion, ultra-long-distance landfill of a solidified substance is further performed through a pumping device, and the method and system are suitable for construction of large-scale sea mud solidification projects; the sea mud is converted through addition of a curing agent into the solidified substance which is similar to soil and has high cementing strength and no secondary environmental pollution, so that harmless treatment of the sea mud is achieved; the sea mud is highly dispersed into a dispersion with low-viscosity or good rheological properties through addition of a conditioning agent, and meanwhile since an adsorption electric double layer can be formed uniformly on the surface of the material through a dispersant, the tendency of secondary flocculation and agglomeration of sea mud particles is reduced greatly, so that the stability of the dispersion is improved, and the pumping capacity of the solidified sea mud is also improved at the same time; and according to the system for modifying treatment of the high-viscosity sea mud, transportation is carried out through containers, the system has continuous operation, high efficiency and adaptability to on-site treatment, and harm to the environment can be avoided.