This study presents fabrication of bi-compartmental particles labeled by multiple fluorescence. To compartmentalize fluorescent expression at the particle, two fluorescent dyes with less overlap of the excitation and emission spectra are selected. To ensure the fluorescence stability, the fluorescent dyes contain acrylate functional groups in the molecules so that they can be cross-linked together with monomers constituting the particle. Strong fluorescent expression and compartmentalization were observed at the particle fabricated using the selected fluorescent dyes through confocal microscopy. Furthermore, long-term fluorescence stability was verified by measuring fluorescent expression and intensity for 4 weeks. We anticipate that the bi-compartmental particles labeled by multiple fluorescence can be widely used for multi-target drug delivery system, analysis of 3 dimensional Brownian motion, and investigation of 3 dimensional complex self-assembled morphologies.