The invention provides a gel water shutoff agent of a high-temperature low-permeability storage layer. The gel water shutoff agent of the high-temperature low-permeability storage layer comprises the following components: 2-20wt% of a host, 0.5-5wt% of a cross-linking agent and the balance of water, wherein the host comprises a host A and a host B; the host A comprises 2-acrylic acid-1,1-dimehtyl ethyl ester, 2,2-bis(3,5-dibromo-4-hydroxyl phenyl) propane, 2, 2', 6, 6'-tetrabromobisphenol A; the host B comprises acrylamide, hydrolytic polyacrylamide or non-hydrolytic polyacrylamide, wherein a mass ratio of the host A to the component B is 1 to (1-2). The gel water shutoff agent provided by the invention is suitable for the high-temperature low-permeability storage layer and low in base fluid viscosity, and is easily injected to the deep part of the low-permeability storage layer, and has good viscosity, high tensile strength, high adhesive power, good high temperature resistance and good thermal stability after being cross-linked.