Novel nanocomposites with good electromagnetic interference (EMI) shielding efficiency were prepared in-situ from thermosetting polybenzoxazine (PBZ) and trichlorophenylsilane modified graphene (GS). The pristine globular graphene (G) was intercalated by trichlorophenylsilane and formed more single layer graphene, which was verified by TEM images. Good dispersion of GS decreased the percolation threshold to less than 1 wt%. The conductivity increased greatly and reached 0.0032 S/cm with the addition of 20 wt% of GS, and the corresponding nanocomposites showed the highest shielding effectiveness (SE) of 40.9 dB over the range of X-band. And the SE was found to be dominated by absorption, which could effectively reduce the secondary pollution of electromagnetic wave. Additionally, the mechanical strength, storage modulus at rubbery state, and chemical cross-linking density were highly improved by the addition of GS.