Thermally conductive polymer composites, in particular those composed of polymers and carbon-based nanomaterials, are promising for thermal management in electronic devices because they offer high thermal conductivity at low loading of filler. The effective thermal properties of these composites exhibit high variability that depend on the topological arrangements and the morphological characteristics of the filler particles. In order to tailor the thermal conduction within these composites for their use as an efficient heat dissipation material, careful control of the microstructural arrangement of the filler material is required. In this work, we use infrared microscopy to characterize thermal transport through epoxy composites containing submillimeter sized graphitic flakes as filler particles. Filler particle shape, size and dispersity (in shape and size) can impact thermal conduction. Graphite flake-epoxy composites of two volume fractions are prepared and characterized using an infrared microscope with a temperature resolution of that images the temperature distribution at the top surface of the composite subject to a temperature gradient. The effective thermal conductivity of the composite with a filler fraction was found to be, a factor of 16 higher than the neat epoxy. With the micron-scale resolution of the IR microscope, the steady state particle-scale temperature fields within the composite are directly observed and highlight the non-uniform heat transfer pathways. This local temperature analysis reveals important microstructural features such as percolation and clustering of filler particles. Finally, shear-induced microstructural alignment can potentially be revealed from anisotropic heat flow within the composite. This study forms the basis for future investigation of shear-induced alignment of platelet-like graphitic particles, control of viscosity of the polymer, and contributes towards the development of novel processing methods, such as rheological processing of polymeric suspensions, to fabricate materials with tailored thermal properties for application in electronics heat dissipation.