Provided are an organically modified silica master batch elastomer having superior affinity for silica and a method for preparing the same. A copolymer solution-polymerized from a conjugated diene-based monomer and a vinyl aromatic monomer is mixed in solution with organically modified silica having the silica modified with a specific aliphatic hydrocarbon to prepare the organically modified silica master batch elastomer. The organically modified silica master batch elastomer according to the present invention has improved mechanical properties, abrasion resistance and blending processability over the existing master batch elastomers containing common silica. Thus, when it is used as a tire material, improved fuel efficiency, abrasion resistance and wet traction may be expected.