Magnetic fluorescent nanomaterials have broad application prospects as taggants in fields such as anticounterfeiting identification, suspicious object tracking, and potential fingerprint recognition in forensic medicine. It is a common method to synthesize magnetic fluorescent composite nanoparticles by preparing a shell on the surface of magnetic particles to load fluorescent materials. In this work, a magnetic fluorescence nanohybrid was synthesized by in situ encapsulation of carbon quantum dots (CQDs) during the preparation of a SiO2 shell on the surface of Fe3O4 nanoparticles. The traditional Stöber method was employed to synthesize the SiO2 shell. Meanwhile, CQDs were introduced into the hydrolysis process of tetraethyl orthosilicate. To address the issue of charge repulsion between the negatively charged hydrolysis intermediate of tetraethyl orthosilicate and the negatively charged CQDs, poly(diallyldimethylammonium chloride) with positive charge was introduced in the synthesis process. The repulsive charges in the reaction system were balanced by poly(diallyldimethylammonium chloride), allowing for the successful encapsulation of CQDs in the SiO2 shell. The structure, morphology, and magnetic and fluorescence properties of the prepared Fe3O4@SiO2-CQDs were characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, a vibrating sample magnetometer, and a fluorescence spectrophotometer. The Fe3O4@SiO2-CQDs exhibited excellent magnetic and fluorescence properties, making them suitable for fluorescence labeling on various substrates and showing great potential in labeling, tracing, and fluorescence sensors.