A system for measuring small oil droplets in an oil-in-water (O/W) emulsion was developed using multiphoton ionization time-of-flight mass spectrometry. In the present study, a capillary column with an inner diameter of 15 µm was used for sample introduction. Moreover, a compact microscopic system was constructed for observing an emulsion flowing through a capillary column. As a result, the length for sample introduction was shortened, which is preferable for the direct evaluation of an emulsion. Using this system, the minimum diameter of a detectable toluene droplet in an O/W emulsion was decreased to 1.7 µm. The present system could be used to evaluate the local microenvironment and stability of an emulsion.