Ball milling is adopted to uniformly reduced the critical dimensions of the low cost chemically exfoliated graphite nanoplatelets (EGN) and embedded into the matrix of flexible polydimethylsiloxane (PDMS) for thermal interface materials (TIMs) applications. In this work, we report a method for the particle size reduction of EGN into high-quality fillers of ball-milled exfoliated graphite nanoplatelets (BMEGN) and thermally cured with PDMS to make a highly stretchable BMEGN-embedded PDMS-TIMs (BMEGN/PDMS) with improved thermal conductivity and mechanical properties. The thermal conductivity was experimentally measured for BMEGN fillers with 0–4 h ball milling time. A maximum in-plane thermal conductivity of 14.7 W/mK and through-plane thermal conductivity of 0.88 W/mK was found. Furthermore, the mechanical properties allowing the developed TIMs to bend, fold, stretch or conform to the user-specified environment, exhibits synergetic mechanical properties with outstanding flexibility. The prepared TIMs were further characterized by scanning electron microscopy, thermogravimetric analysis, and X-ray diffraction.