Heterogeneous magnetic nanocatalyst, Fe3O4@SiO2–Ligand–Cu (II) MNPs, reveals high catalytic performance within the synthesis of propargylamines using the multicomponent coupling reaction of aldehydes, phenylacetylene and secondary amines in water as a solvent. The substantial feature of this organic–inorganic hybrid magnetic nanocatalyst is the capability of straightforward separation of the reaction mixture by an external magnet which was retrieved ten times without significant loss of catalytic activity. This methodology has other advantages such as subordination to the principles of green chemistry and avoiding the use of expensive and harmful organic solvents. To study the stability and actual structure of birhodanine derivative–copper (II) complex, DFT calculations were also performed.