Terahertz (THz) time-domain spectroscopy (TDS) is a recently emerging analysis method which can provide unique information on molecular vibration and rotation induced by inter/intra-molecular interactions. Although the application of THz-TDS to high-performance microscale separation methods like capillary electrophoresis (CE) has been anticipated, it has been hindered due to the diffraction limit of THz wave (typically, hundreds µm). In order to realize CE-THz-TDS, in this study, we placed a narrow open-tubular capillary on the surface of a GaAs semiconductor substrate as a “localized” THz-emitter. By focusing femtosecond pulsed laser beams at the surface of a gallium arsenide (GaAs) substrate closest to the capillary, THz waves were locally generated to pass through the capillary, so that THz absorbance spectra were obtained from the capillary which has narrower inner diameter than the diffraction limit. As a typical result from acetic acid analysis in the CE-THz-TDS platform, information on the refractive index and extinction coefficient was obtained, which showed non-linear and linear concentration dependence, respectively, similar to conventional THz-TDS using large liquid cells. Finally, CE-THz-TDS analysis of several carboxylic acids was demonstrated. Two acids were successfully separated and detected with THz-TDS, where their electrophoretic mobility values were estimated as close to those obtained with conventional contactless conductivity detection. Our proposed CE-THz-TDS showed the potential for the systematic analysis of inter/intra-molecular weak interactions like hydrogen bonds, which are unable to obtain with conventional detectors.