Electrophoretic migration of an analyte in capillary electrophoresis (CE) reflects reaction dynamics of the analyte in solution.In affinity CE, an analyte of interest interacts with a modifier added in the separation buffer in fast equilibrium, and effective electrophoretic mobility of the analyte is contributed from its equilibrium species. Precise measurement of effective electrophoretic mobility allows analyzing the equilibrium. Analysis of equilibria under CE separation possesses several advantages against traditional analyses in homogeneous solution; coexisting substances including impurities and kinetically generated substances are resolved by CE from the equilibrium species of interest. Characteristics of the CE analysis have been applied to analyses of acid-base equilibria of degradable substances and ion-association equilibria in an aqueous solution. Since CE is operated in an open-tubular capillary, it is also suitable for the characterization of carbon nanoclusters such as graphene and carbon nanotube, and measurement of effective electrophoretic mobility helps characterization of nanoclusters. A novel analysis technique of capillary electrophoresis/dynamic frontal analysis (CE/DFA) has also been proposed for the analysis of such reactions as involving equilibria and kinetic reactions. In CE/DFA, kinetically generated product is continuously resolved from the equilibrium species, and a plateau signal would be detected when the reaction rate is constant. Michaelis-Menten constants have successfully been determined through the plateau height by CE/DFA. In this review, analysis and characterization methods utilizing reaction dynamics in a separation capillary are summarized.