A new class of high stable, dual fluorescent encoding magnetic composite nanoparticle has been synthesized via reverse microemulsion method. Two kinds of CdTe QDs with different emission wavelengths and magnetic nanoparticles (Fe3O4) were embedded in silica nanoparticles at precisely controlled ratios. In this process, superparamagnetic Fe3O4 nanoparticles and one kind of QDs (573 nm) as cores were coated with silica, forming the first core-shell structure magnetic fluorescent nanoparticles (MFNs); then the MFNs and the other kind of QDs (653 nm) as cores were coated with another silica shell to form the fluorescent, magnetic dual core-shell encoding composite nanoparticles. With the aim of embedding more QDs in MFNs, we use poly(dimethyldiallyl ammonium chloride) to balance the electrostatic repulsion between QDs and silica intermediates. A surface-active reagent, 3-aminopropyltrimethoxysliane was used to link the MFNs with QDs and terminate the surface of composite nanoparticles. Finally, by modifying the surface of composite nanoparticles with amino groups and methylphosphonate groups, biologically functionalized and monodispersed composite nanoparticles were obtained.