Heat treatment is a promising pre-processing method in the conversion of kraft lignins to carbon fibers. In this study, a kraft lignin was subjected to heat treatment at different lengths of time and at different temperatures. The molecular structure of the untreated and four heat treated lignins were investigated mainly by a variety of nuclear magnetic resonance spectroscopy (NMR) methods. The results were compared to structural information obtained by pyrolysis-gas chromatography-/mass spectrometry (py-GC/MS) and Fourier transform infrared spectroscopy (FTIR). It was observed that during the thermal treatment, the amount of β-O-4 ether moieties decreased, and an intramolecular conversion of secoisolariciresinol residues to cyclic ethers occurred. The effects on shape and size of the lignins were investigated by size exclusion chromatography (SEC) and NMR-diffusion measurements, by which the hydrodynamic radii were found to increase as a result of thermal treatment. It is discussed whether this depends on reduced flexibility and/or increased molar mass. In addition, the trends from the SEC and NMR analyses were compared to changes in glass transition temperature as determined by differential scanning calorimetry (DSC).