In the past decade, fluorescence correlation spectroscopy (FCS) has become an ultrasensitive and noninvasive single-molecule detection technique, which is widely applied in the physical, chemical, and life-science research. The coupling of FCS with narrow channel flow systems including the ones based on capillary provide the important, convenient, and sensitive assay platforms for probing and understanding the behavior of single molecules or nanoparticles with improved temporal and spatial resolution and need for less sample volume among other advantages. This review focus on different approaches for FCS with capillary and microchannel analytical systems and its applications in confined diffusion study, flow profiles, and imaging of narrow channel, multicomponent analyses such as protein, DNA analysis, and characterization on nanoparticles.