The combination of a bulk 3D perovskite layer and a reduced dimensional perovskite layer (perovskite quantum wells (PQWs)) is demonstrated to enhance the performance of perovskite solar cells (PSCs) significantly in terms of stability and efficiency. This perovskite hierarchy has attracted intensive research interest; however, the in-depth formation mechanism of perovskite quantum wells on top of a 3D perovskite layer is not clearly understood and is therefore the focus of this study. Along with ex situ morphology and photophysical characterization, the time-resolved grazing-incidence wide-angle X-ray scattering (TS-GIWAXS) technique performed in this study provides real-time insights on the phase-transition during the organic cation (HTAB ligand molecule) coating and PQWs/3D architecture formation process. A strikingly strong ionic reaction between the 3D perovskite and the long-chain organic cation leads to the quick formation of an ordered intermediate phase within only a few seconds. The optimal PQWs/3D architecture is achieved by controlling the HTAB casting, which is assisted by time-of-flight SIMS characterization. By controlling the second ionic reaction during the long-chain cation coating process, along with the fluorinated poly(triarylamine) (PTAA) as a hole-transport layer, the perovskite solar cells demonstrate efficiencies exceeding 22% along with drastically improved device stability.