The invention discloses a multifunctional concrete structure endurance protective agent as well as the preparation and application method thereof. The protective agent provided by the invention contains the following ingredients of: an organic/inorganic composite fluorosilicone-acrylate copolymer, lithium silicate, sodium silicate, lithium molybdate, sodium tetraborate, sal glauberi, 1,2-aminoazophenylene, nanometer titanium dioxide, anhydrous ethanol and water. The protective agent can penetrate inside concrete, wherein a densification ingredient can minimize internal holes and cracks to raise the compactness of concrete, and a rust-resistant ingredient can penetrate into concrete and be adsorbed on the surface of steel bar so as to passivate and protect the steel bar; the low-surface energy silicon fluoride ingredient can be solidified to form a cured film on the surface of concrete so as to endow the protective agent with the hydrophobic performance; a nanometer ingredient can endow the cured film layer with properties of resisting ultraviolet and ageing and improving the organic polymer performance as well as the self-cleaning performance. In addition, hydroxy generated from the hydrolysis of siloxane group can perform a condensation reaction with hydroxy on the surface of concrete to produce chemical bond, so as to raise the anchoring strength between the film and concrete and improve the interface combination. The protective agent provided by the invention can be widely applied in various concrete structure engineering protections to raise the service life of concrete.