We investigate the microconfinement of charged silica nanoparticles dispersed in refractive index matching monomers in poly(dimethylsiloxane) (PDMS) porous membrane. Here, the silica colloidal particles interact with each other and the pore wall via electrostatic double layer forces. Different from the hard sphere systems where the assembled morphologies are prescribed by the diameter ratio between the cylindrical confinement and the nanoparticles, here we observe a much richer variety of assemblies that are highly sensitive to both bulk and local nanoparticle concentration with fixed particle size and channel size. The experimentally observed assembly morphologies are consistent with theoretical predictions from the literature, based on Yukawa potential in the low packing density regime. Also, most of the configurations found in the experiment are well described by computer simulations using pairwise additive long-range repulsive interactions, demonstrating the ability to control the system to obtain a desired structure.