A fluorescence immunoassay device based on integration of a photonic crystal and magnetic beads and a method thereof are provided. Magnetic beads with high surface-to-volume ratio are used as carriers of fluorescent molecules to obtain higher fluorescence density. The electric field on the surface of the photonic crystal is enhanced through excitation of photonic crystal resonance. The intensity of the fluorescence signal excited by the enhanced electric field is increased. Moreover, through interaction with the photonic crystal, some fluorescent signals that originally cannot be received by the fluorescent sensor are coupled to the photonic crystal resonant modes and reradiate toward the fluorescent sensor, thereby increasing collection efficiency. The fluorescence signals generated by fluorescent molecules on the magnetic beads are significantly intensified, which could lower the detection limit. Furthermore, the magnetic beads aggregation method can achieve the detection capability that cannot be achieved by the current fluorescent immunoassay.