Most two-dimensional (2D) semiconductors suffer from intrinsic instability under ambient conditions, especially 2D black phosphorus (BP). Although much effort has been made to study the passivation of 2D materials against corrosion by oxygen and water molecules, facile and effective passivation with long-Term stability is still challenging; in particular, selective passivation, which is critical for integration into nanoelectronics, is still lacking. Here, we develop a novel passivation route for BP using a fluorinated self-Assembled thin film of PFSA (perfluorosulfonic acid, PFSA), where the surface modifier with high hydrophobicity on BP presents extremely stable characteristics over five months under ambient conditions. Moreover, we report for the first time in situ cleaning and selective fluorination of only BP flakes on a SiO2/Si substrate by a spin-coating process followed by ultrasonication, which was attributed to the formation of P-F covalent bonds on the BP surface. Selectively fluorinated BP shows not only enhanced stability in air but also electrical properties of the BP field-effect transistor (FET), with the on-current of the BP FET increasing and presenting enhanced carrier mobility (125 cm2 V-1 s-1) and on/off ratio (104). This significant finding sheds light on fabricating vertical 2D heterostructures to realize high performance and reliability with versatile 2D materials. This work demonstrates an emerging passivation approach for long-Term stability together with superior electrical properties, which paves the way for integrating 2D semiconductors into critical channel materials in FETs that are favorable for next-generation digital logic circuits.