Because of their synthetic accessibility, molecularly imprinted polymer (MIP) nanoparticles are ideal building blocks for preparing multifunctional composites. In this work, we developed a general photocoupling chemistry to enable simple conjugation of MIP nanoparticles with inorganic magnetic nanoparticles. We first synthesized MIP nanoparticles using propranolol as a model template and perfluorophenyl azide-modified silica-coated magnetic nanoparticles. Using a simple photoactivation followed by facile purification with a magnet, we obtained magnetic composite particles that showed selective uptake of propranolol. We characterized the nanoparticles and composite materials using FT-IR, TEM, fluorescence spectroscopy, and radioligand binding analysis. Through the high molecular selectivity of the magnetic composite, we demonstrated the nondestructive feature and the high efficiency of the photocoupling chemistry. The versatile photoconjugation method developed in this work should also be very useful for combining organic MIPs with other inorganic nanoparticles to enable new chemical sensors and high efficiency photocatalysts.