Cu-doped rod-shaped mesoporous silica nanoparticles (Cu-RMSN) were synthesized by a new one-step approach based on in situ functionalization procedure referring to the phenomenon of micellar solubilization. SEM and TEM studies revealed the rod-like morphology of uniformly sized particles with longitudinal mesopore channels. The BET specific surface areas were near 500 m2 g–1 and the average pore diameter varied from 3 to 3.6 nm. The composite Cu-RMSN proved to be an efficient heterogeneous catalyst for a microwave-assisted three-component 1,3-dipolar cycloaddition reaction in aqueous solution. The one-pot preparation of 1,4-dibustituted-1,2,3-triazole derivatives was straightforward and high yielding, due to the high copper dispersion at the pore surface resulting in the high accessibility of the active sites. The efficiency of the catalyst was also demonstrated upon recycling, making such synthesis a truly green process with marked step and solvent economy and important waste reduction.