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In hybrid perovskites, the organic molecules and inorganic frameworks exhibit distinct static and dynamic characteristics. Their coupling will lead to fascinating phenomena, such as large polarons, dynamic Rashba–Dresselhaus effects, etc. In this paper, deep potential molecular dynamics (DPMD) is employed, a large‐scale MD simulation scheme with DFT accuracy, to study hybrid perovskites formamidinium lead iodide (FAPbI3) and methylamonium lead iodide (MAPbI3). A spontaneous hybrid nano‐domain behavior, namely multiple molecular rotation nano‐domains embedded into a single [PbI6]4− octahedra rotation domain, is first discovered at low temperatures. The behavior originates from the interplay between the long range order of molecular rotation and local lattice deformation, and clarifies the puzzling structural features of FAPbI3 at low temperatures. The work provides new insights into the structural characteristics and stability of hybrid perovskite, as well as new ideas for the structural characterization of organic–inorganic coupled systems. [ABSTRACT FROM AUTHOR]