Fe single‐atom catalysts (Fe‐SACs) have been extensively studied as a highly efficient electrocatalyst toward the oxygen reduction reaction (ORR). Nonetheless, they suffer from stability issue induced by dissolution of Fe metal center and the OH− blocking. Herein, a surface molecular engineering strategy is developed by using β‐cyclodextrins (CDs) as a localized molecular encapsulation. The CD‐modified Fe‐SAC (Fe‐SNC‐β‐CD) shows obviously improved activity toward the ORR with 0.90 V, 4.10 and 4.09 mA cm−2 for E1/2, J0 and Jk0.9, respectively. Meanwhile, the Fe‐SNC‐β‐CD shows the excellent long‐term stability against aggressive stress and the poisoning. It is confirmed through electrochemical investigation that modification of β‐CD can, on one hand, regulate the atomic Fe coordination chemistry through the interaction between the CD and FeNx moiety, while on the other mitigate the strong adsorption of OH− and function as protective barrier against the poisoning molecules leading to enhanced ORR activity and stability for the Fe‐SACs. The molecular encapsulation strategy demonstrates the uniqueness of post‐pyrolysis surface molecular engineering for the design of single‐atom catalyst.