A novel surface-modified silicon-based thermal management technology has been proposed for 3D IC architecture in this study. 2 × 2 cm2 double sides polished silicon chips’ surface with micro-fin (MF) and micro-pin fin (MPF) structures have been achieved by applying silicon microfabrication technology of deep reactive ion etching, which is applicable to the interlayer of 3D IC packaging technology. By integrating a mini wind tunnel with Raman spectrometer, the transient thermal property measurement system is originally designed to evaluate the cooling capability of the surface-modified silicon interlayer. Finite Element Analysis was involved to confirm this view by taking fluid dynamics and heat transfer into account. The sample with 100 × 100 µm2 MPF structure expresses the appropriate exponential decay time constant τ (with unit of 1), which is 4.71 and 8.53 under cooling and heating measurement conditions, respectively. This also proved that the combination of Raman thermometry with forced gas flow could be a relevant measurement tool for transient thermal property.