The invention discloses a cross-linked polymer system heat stabilizer for water shutoff and profile control, and a preparation method and application thereof, wherein the heat stabilizer is composed of the following components in parts by weight: 2-8 parts of sodium thiosulfate, 30-50 parts of polyethylene glycol, 10-30 parts of urea, 1-5 parts of formaldehyde and 800-1200 parts of de-ionized water. All of the components are evenly mixed to obtain the heat stabilizer which is used as a cross-linked polymer system common in water shutoff and profile control or profile control and displacement of the oil field; and the cross-linked polymer system is composed of polyacrylamide aqueous solution and a phenolic resin cross-linking agent or organic chromium cross-linking agent. The thiourea or sodium thiosulfate of the heat stabilizer provided by the invention serves as the deoxidant, the polyethylene glycol or the urea serves as the complexing stabilizer, and the formaldehyde serves as the complexing stabilizer and the bactericide; the method for preparing the cross-linked polymer system heat stabilizer is simple and the use cost is also low; therefore, the strength and the stability of the cross-linked system both can be well improved.