One object of the invention is to improve the affinity between the silicone resin and the thermally conductive filler to facilitate mixing thereof. Another object of the invention is to suppress a viscosity increase of a silicone resin composition containing a high level of loading of thermally conductive filler, and to provide a cured product having a higher thermal conductivity. According to the invention, a thermally conductive silicone composition is provided, which comprises (A) an organopolysiloxane having two or more alkenyl groups each bonded to a silicon atom per molecule; (B) an organohydrogenpolysiloxane having two or more hydrogen atoms each bonded to a silicon atom per molecule in such an amount that the molar ratio of the hydrogen atoms each bonded to a silicon atom in component (B) to the alkenyl groups in component (A) is within the range of from 0.1 to 4; (C) 50 to 98% by mass, based on total weight of the composition, of a thermally conductive filler; and (D) a catalytic amount of a catalyst based on a platinum group metal, wherein the thermally conductive filler has a contact angle with water of at most 75° on the filler surface.