We developed a microscope by a combination of synchrotron radiation X-ray fluorescence (SR-XRF) microscope and scanning electron microscope (SEM) with an energy dispersive X-ray spectrometer (EDX). SR-XRF is appropriate to detect trace and micro amount of elements and sensitive to heavy elements in an analyte but it cannot observe the real time image. SEM-EDX can observe the secondary electron image of a single particle in real time and is appropriate to detect lighter elements. This combination microscope can ensure the identification of the XRF spectrum to the SEM image without transferring the sample. For aerosol analysis, it is important to analyze each particle. The present method makes feasible to analyze not only the average elemental composition as the total particles but also elemental composition of each particle, which is dependent on the particle shape and size. The microscope was applied to an individual aerosol particle study. The X-ray spectra were different among the particles, but also different between SR-XRF and SEM-EDX for the same particle, due to the difference in fluorescence yields between X-ray excitation and electron excitation.