The invention provides a modified paste filler which is prepared from 1%-7.5% w/w of DMADDM and 92.5%-99% w/w of hydrophilic methacrylate sealing agent. The invention further provides a preparation method and application of the paste filler. According to the invention, by taking multiple performances such as the antibacterial property of the composite material and cytotoxicity and solubility as indexes, the dosage relation of DMADDM and EdnoREZ is researched, the influence of the dosage relation of the two to the antibacterial property and sealing property of the composite material is inspected, and finally a proper dosage relation is screened out by an experiment, so as to meet the maximization of the antibacterial property and the sealing property, thus achieving the purpose of preparing the novel resin type root canal paste filler material with effective antibacterial property, and solving the problem that paste fillers in the current dental material markets do not have obvious antibacterial property.