The invention relates to a high-temperature high-salinity oil reservoir polymer microsphere dispersed system modifying and flooding agent, and a preparation method and an application thereof. In prior arts, polymer microsphere system prepared with an inverse emulsion method has low compounding performance with a flooding surfactant, such that chromatographic separation might occur after long-term aging, and flooding efficiency is reduced. The high-temperature high-salinity oil reservoir polymer microsphere dispersed system modifying and flooding agent provided by the invention comprises the following components, by weight: 0.3-3 parts of a polymer microsphere dispersed system, 0.5-5 parts of a flooding surfactant, and 92-99.2 parts of water. The dispersed system is polymer microsphere with an submicron-grade to micron-grade initial particle size and with monodispersity, prepared with an alcohol-water system dispersion polymerization method. According to the invention, the above problem is well solved. The high-temperature high-salinity oil reservoir polymer microsphere dispersed system modifying and flooding agent can be applied in on-site high-temperature high-salt-infiltration oil reservoir tertiary oil recovery deep profile control, water plugging and flooding applications for improving recovery rate.