FAPbI3 (FA+ = formamidinium) perovskite, one of the most efficient basic components in nowadays perovskite solar cells (PCSs), undergoes spontaneous phase transition while molecular-level investigations are still lacking. Here, we report a structural study on the phase transition process of the FA-based perovskites based on isolation and identification of a series of single crystal intermediates. A key intermediate of 8H phase with unique structure is discovered, which helps elucidate the complete phase evolution and stabilization mechanism of FA-based perovskites. Our new insight based on the Pauling’s rules not only deepens the understanding of the phase stabilization roles of cations and anions in maximizing the concentrations of corner-sharing halogens and cubic cages but also forms suggestion for fabrication of high-performance and long-term stable PCSs by controlling the factors such as composition, precursor solution, stoichiometry, and additives.