Supercritical fluid extraction (SCFE) is gaining significant interest as a green technology for the recycling of end-of-life waste electrical and electronic equipment (WEEE). Neodymium iron boron (NdFeB) magnets, which contain large quantities of critical rare-earth elements such as neodymium, praseodymium, and dysprosium, are widely used in wind turbines and electric/hybrid vehicles. Hence, they are considered a promising secondary resource for these elements when they reach their end-of-life. Previously, the SCFE process was developed for recycling WEEE, including NdFeB; however, the process mechanism remains unexplored. Here, density functional theory, followed by extended X-ray absorption fine structure and X-ray absorption near-edge structure analyses, are utilized to determine the structural coordination and interatomic interactions of complexes formed during the SCFE of the NdFeB magnet. The results indicate that Fe(II), Fe(III), and Nd(III) form Fe(NO3)2(TBP)2, Fe(NO3)3(TBP)2, and Nd(NO3)3(TBP)3 complexes, respectively. This theory-guided investigation elucidates the complexation chemistry and mechanism during the SCFE process by rigorously determining the structural models.