A picosecond near-field microspectroscopy system was developed and applied to fluorescence analysis of charge transfer (CT) microcrystals. Fluorescence spectra and decay curves of anthracene/tetrachlorophthalic anhydride/pyromellitic dianhydride (anthracene/TCPA/PMDA) mixed microcrystals were measured with a resolution of ~140 nm. Sub-μm-sized domain structures were observed, and fluorescence spectra and decay curves were different in the domains. Some domains with a common fluorescence spectrum but with different decay curves were observed, indicating an inhomogeneous distribution of quenching sites. New features of inhomogeneity of CT crystals are presented and considered.