Nanoscale polymer silica hybrid nanochannels of average channel size of ~50 nm are fabricated by electrokinetically induced silicification reaction within a polymer template. The uniform growth of silica can be realized by appropriate combination of reactant concentration and electric field strength. The formed silica leads to the reduction in channel size, and provides substantial reinforcement to the polymer nanostructure. Analog 2D microfluidic devices are also constructed to visualize and study the mechanism of the dynamic assembly process with fluorescence labeled nanoparticles. The dynamic complexation was carried out and quantified by recording and measuring fluorescence intensity along the channel wall. It was found that the complexation started from the small end first and extends gradually towards the large end. Recirculation flows were observed both inside (close to the channel surface) and outside (at the small end) the converging channel. A two-stage complexation was observed and the primary complexation happened in the stagnation region between a vortex pair. Dynamic complexation continued generating non-uniform zeta potential along the channel surface and gave rise to the moving of vortex pair towards the large end.