The function of a protein correlates closely with its structure; even partial structural disorder/misfolding may lead to various diseases such as Parkinsons disease. Therefore, analysis of the local structure of a protein (e.g., detecting conformation changes during folding/unfolding, and obtaining the information on local polarity, viscosity, etc.) is of great importance for proteomics studies, and in this respect fluorescence spectroscopy plays a crucial role because of its great temporal and spatial sampling capability. In particular, fluorescent probes combined with a site-specific labeling technique have been widely used in structural analysis of proteins due to their powerful ability in the elucidation of various properties and functions of proteins. The developments of excellent spectroscopic probes as well as site-specific labeling methods are the prerequisites for conducting such a kind of study. Herein we review the progress and use of N-terminal specific labeling and fluorescence probes in local structure analysis of proteins, including some results of our recent studies on α-lactalbumin, β-lactoglobulin, and a dimeric protein of DsbC.