The femtosecond fluorescence up-conversion microscope has been developed. This new method was applied to the study of exciton dynamics in an organic microcrystal, perylene. Taking advantage of femtosecond time-resolution and nanometer space-resolution, the fluorescence from microcrystals was clearly time-resolved and the ultrafast relaxation dynamics of the free exciton and the Y state was clarified at room temperature. It was found that the exciton dynamics significantly depends on the position in the microcrystal, reflecting the spatial distribution of the defect.