The invention relates to a branched chain functionalized styrene-butadiene-styrene block copolymer (SBS) and a preparation method thereof as well as application of the branched chain functionalized SBS in modified asphalt. The grafted functionality degree (FD) of the branched chain functionalized SBS is 4 to 60mol percent. The preparation method comprises the following steps: dissolving the SBS and sulfydryl compounds containing polar groups into an organic solvent at the temperature of 15 to 70 DEG C; then adding an initiator, and performing side chain functionalization reaction at the reaction temperature of 40 to 100 DEG C for 0.5 to 20 hours; after the reaction is ended, adding a cross-linking promoting agent and a plasticizer; precipitating and drying to obtain functionalized SBS with different branched chains; applying the functionalized SBS to the modified asphalt. Compared with the prior art, the method disclosed by the invention has the advantages of simplicity, mild reaction conditions, high efficiency in reaction and high selectivity, and can be used for producing large-scale dose. A prepared product has a wide application prospect, can be used for producing shoes and waterproof roll industries, or can be used as a modified additive in blending modification of a polymer, and is particularly suitable for modified asphalt operation of roads; the dispersibility and the compatibility of the SBS in the asphalt can be remarkably improved, the heat storage stability of the modified asphalt is improved, and high-performance modified asphalt is prepared.