Fe3C/C nanohybrid has a wide application in many fields due to its versatility in numerous scenarios, however, the need for precise control of nanostructure is the obstacle during high-temperature pyrolysis of iron–nitrogen precursor. The purpose of this study was to explore the formation process and formation dynamic of Fe3C/C nanohybrid via pyrolysis. Based on in-situ (TGA-MS, TGA-FTIR) and ex-situ characterization (XRD, Raman, HR-TEM, Mössbauer, XAFS), the self-assembled ‘laminated template CxNy’ involved nucleation was crucial for the formation of Fe3C/C nanostructure. It enabled the dispersion of iron atoms at the molecular level and the nucleation of Fe(NCN) at the nanoscale. Moreover, the effects of temperature programming were evaluated by the peroxymonosulfate (PMS) activation efficiency towards bisphenol A (BPA) degradation. Fe0/Fe3C/C prepared with a heating rate of 3.5 °C/min during nucleation was proven to have the optimum PMS activation performance (1O2 and ·OH pathway), owing to Fe3C mediator is able to modulate the electronic structure of carbon as well as the corrosion rate of Fe0. This finding of nucleation and growth process would be valuable for the structure-controlled synthesis of Fe0/Fe3C/C in the large-scale.