Van der Waals (vdW) atomically thin materials and their heterostructures offer a versatile platform for the management of nanoscale heat transport and the design of novel thermoelectrics. These require the measurement of highly anisotropic heat transport in vdW‐based nanolayers, a major challenge for nanostructured materials and devices. In the present study, a novel effective method of cross‐sectional scanning thermal microscopy was used to map and quantify the anisotropic heat transport in nanoscale thick layers of vdW materials and the material‐substrate interfaces. This technique measures the heat conducted into a vdW crystal via the nanoscale apex of a heat‐sensitive probe. The crystal is nano‐polished via Ar ion beams generating an oblique nearly atomically flat surface. By measuring the thermal conductance variation as a function of increasing layer thickness, the transition between the cross‐plane and in‐plane heat transport (defined by heat conductivity anisotropy) is acquired. By using an analytical model validated by finite element simulations, anisotropic thermal transport in a gamma indium selenide crystal nano‐thin flake on a Si substrate was studied, obtaining results corresponding to anomalously low anisotropic thermal conductivities of kxy = 2.16 Wm−1 K−1 in‐plane and kz = 0.89 Wm−1 K−1 cross‐plane confirming its potential for thermoelectric applications.