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Understanding the energy transport by charge carriers and phonons in two-dimensional (2D) van der Waals heterostructures is essential for the development of future energy-efficient 2D nanoelectronics. Here, we performed in situ spatially resolved Raman thermometry on an electrically biased graphene channel and its hBN substrate to study the energy dissipation mechanism in graphene/hBN heterostructures. By comparing the temperature profile along the biased graphene channel with that along the hBN substrate, we found that the thermal boundary resistance between the graphene and hBN was in the range of (1–2) 10−7 m2 K W−1 from ~100 °C to the onset of graphene break-down at ~600 °C in air. Consideration of an electro-thermal transport model together with the Raman thermometry conducted in air showed that a doping effect occurred under a strong electric field played a crucial role in the energy dissipation of the graphene/hBN device up to T ~ 600 °C.