The development of silica‐filling elastomers with high mechanical performance and good processability is still a great challenge. In this study, we fabricated siloxane‐grafted atactic 1,2‐polybutadiene (1,2‐PB) rubber through grafting poly(1,3‐butadiene)‐block‐(dimethylsiloxane) (PB‐b‐PDMS) onto 1,2‐PB molecular chains by coordination polymerization using a molybdenum (Mo)‐based catalyst system. The PB‐b‐PDMS with active double bonds was synthesized by anionic polymerization. Fourier transform infrared analysis (FTIR), elementary analysis, and GPC‐MALLS‐viscometer analyses verified the incorporation of PB‐b‐PDMS and the grafting structure in the resulting polymer. Scanning electron microscope (SEM), bound rubber testing, and dynamic mechanical analysis demonstrated that the graft‐modification with PB‐b‐PDMS improved silica dispersity in the 1,2‐PB matrix because the incorporation of siloxane groups provided stronger interfacial interaction with silica. Meanwhile, the graft‐modified 1,2‐PB exhibited lower Mooney viscosity, higher tensile strength, and lower heat build‐up than unmodified 1,2‐PB. This concept provides novel inspiration for the preparation of advanced rubber with promoted silica compatibility and mechanical performance.