The superior radiation tolerance of silicon-on-insulator (SOI) wafers makes them critical for next-generation integrated circuit and micro-electro-mechanical system electronics in space technology and nuclear energy, and yet the inherently low thermal conductivity buried oxide layer severely impedes thermal management in SOI-based radio frequency/power devices. While diamond offers exceptional thermal conductivity to enhance heat dissipation, its significant thermomechanical mismatch with silicon poses major challenges to reliable hetero-integration. Here we demonstrate a novel silicon film-on-diamond (SOD) heterostructure using microtransfer printing (μTP) technology, with comparative analysis against surface activated bonded silicon-on-silicon carbide (SOC) and conventional SOI wafers. The μTP-SOD samples exhibit near-zero residual stress (0.026 GPa) in the transferred Si layer and substantially reduced interfacial thermal resistance (ITR) compared to conventional SOI and SOC wafers. Integrated analysis of interfacial microstructures and molecular dynamics simulations reveals how interfacial structures and amorphous compositions govern the phonon thermal transport. Particularly, the amorphous SiO-SiC transition layer enhances phonon transmission at the μTP-SOD heterointerface to achieve a low ITR of 6.3 + 1.6/–1.5 m²·K/GW. Finite element analysis verifies that these interfacial enhancements, combined with the diamond’s exceptional thermal conductivity, reduce the device junction-temperature rise by 66.7% relative to SOI devices at 15 W/mm output power. The low residual stress and reduced ITR of μTP-SOD are expected to provide promising thermal management schemes for SOI-based electronics.