Abstract Based on hybrid orbital theory, valence shell electron pair repulsion theory, delocalized π bond and examples, this article summed up methods of distinguishing different configurations of the same atom with lone pair valence electrons in molecules. Atom may have three kinds of hybridization such as sp1, sp2, sp3 when it has two or three pairs of lone electrons (e.g.F), if the central atom bonded to it is sp1, sp2, sp3 hybridization,the atom itself is also sp1, sp2, sp3 hybridization respectively, and corresponding examples are HC≡CF, H2C=CHF and CH3F. Atom with only one pair of lone electrons(e.g.N)can have two kinds of hybridization including sp2 and sp3; If the central atom bonded to it is sp1 or sp2 hybridization, the atom itself is sp2 hybridization, such as HC≡CNH2 and H2C=CHNH2; If the central atom bonded to it is sp3 hybridization, the atom itself is also sp3 hybridization, such as CH3NH2. This article also discussed the applying scope of the method and described the application of the method with examples.