The influence of the content of a hydrophilic Pd(II) compound (disodium tetrachloropalladate, Na2PdCl4) on its adsorption and nanoparticle (NP) formation in the pores of hydrophobic micro/mesoporous hypercrosslinked polystyrene (HPS) was systematically investigated. The morphology and composition of HPS-Pd nanocomposites were studied using transmission electron microscopy, X-ray fluorescence measurements, and liquid nitrogen physisorption. The size of Pd-containing NP was found to depend on the content of the hydrophilic Pd(II) compound. Catalytic testing of these nanocomposites in the partial hydrogenation of acetylene alcohols was carried out to illustrate the influence of the NP size on the catalytic activity. The highest catalytic activity was achieved for HPS/Pd-0.1%, forming small NP.