The invention discloses a protective agent for a bridge with a steel structure, a preparation method thereof and application thereof. The protective agent comprises the following components: an organic / inorganic composite fluorosilicone styrene polymer, lithium silicate, sodium molybdate, benzotriazole, nanometer titanium dioxide, sodium gluconate, ethanolamine, absolute ethanol and distilled water. Corrosion inhibiting ingredients contained in the protective agent can be attached to the metal surface of the bridge with the steel structure, so that a compact protective film is formed on the metal surface due to a passivating reaction for corrosion inhibition and corrosion prevention; a low-surface energy fluorosilicone styrene polymer component contained in the protective agent can be cured to form a film for playing the hydrophobic and protective roles; a nanometer component can improve the performance of ultraviolet aging resistance of a film layer, improve the performance of the polymer and provide the excellent self-cleaning performance and the like for the cured film; and hydroxyl generated by hydrolyzing siloxane groups can perform a condensation reaction with hydroxyl on the surface of the bridge with the steel structure to generate a chemical bond so as to improve adhesive power between the film layer and a matrix material and improve interface bonding. The protective agent is high in stability, non-toxic, environment-friendly, multiple in functions and easy to construct, can be widely used for the protection of the structural engineering of various bridges with the steel structures, and is favorable for improving the service life of the bridge with the steel structure.