A good understanding of membrane protein folding at the molecular level requires an effective means to determine the dynamical structural changes on coil-to-helix transition within cell membrane, yet remains challenging. Herein, we demonstrate that the amide III spectral signals of protein backbone, generated in the sum frequency generation vibrational spectroscopy, are a powerful tool to probe the protein folding processes within the membrane in situ, in real time and without exogenous labels. The amide III signals are capable of separating the spectral profiles of the random-coil and α-helical structures at the interface. The intensity ratio of coil and helix peaks becomes a prime indicator that allows to directly capturing the dynamical change of the coil-helix transition. With this approach, using pardaxin as model, the influence of lipid charge on the peptide folding degree at cell membrane surface has been nicely elucidated. It is evident that negative charge of lipid increases the folding degree of pardaxin upon interfacial adsorption and promotes the formation of α-helical structure during the insertion of peptide into lipid bilayer. This robust spectral approach can thus greatly enhance our ability to monitor the dynamics of membrane proteins in a real cell environment in situ.