The development of pore and fracture networks at the nano-scale as a response to heating can reveal coupled physical relationships relevant to several energy applications. A combination of time-lapse 3D imaging and finite-element modelling (FEM) was performed on two typical thermally immature shale samples, Kimmeridge Clay and Akrabou shale, to investigate thermal response at the nm-scale for the first time. Samples were imaged using Transmission X-ray Microscopy (TXM) with a voxel resolution of 34 nm at the I13–2 beamline at Diamond Light source, UK. Images were taken after heating to temperatures of 20 °C, 300 °C, 350 °C and 400 °C. The initiation of nano-pores within individual minerals and organic matter particles were observed and quantified alongside the evolution from nano-pores to micro-fractures. The major expansion of pore-volume occurred between 300 and 350 °C in both samples, with the pores elongating rapidly along the organic-rich bedding. The internal pressures induced by organic matter transformation influenced the development of microfractures. Mechanical properties and strain distributions within these two samples were modelled under a range of axial stresses using FEM. The results show that the overall stiffness of the shale reduced during heating, despite organic matter becoming stiffer. The varied roles of ductile (e.g., clay minerals, organic matter) and brittle materials (e.g., calcite, pyrite) within the rock matrix are also modelled and discussed. The configurations of organic matter, mineral components, porosity and connectivity impact elastic deformation during shale pyrolysis. This work extends our understanding of dynamic coupled processes of microstructure and elastic deformation in shales to the nm-scale, which also has applications to other subsurface energy systems such as carbon sequestration, geothermal and nuclear waste disposal.