Quite recently, we reported the synthesis of supercharged polycations bearing pH-insensitive double-charged repeat units with either three or five methylene groups in the space between charges. The developed approach is based on the quaternization of the parent poly(4-vinylpyridine) with different alkylating agents, providing the possibility to perform the modification as a one-step reaction, which occurs in mild conditions with a controllable degree of conversion. In the present work, we used the above approach for preparing and investigating supercharged polyplexes (polyelectrolyte complexes of nucleic acids), in particular to elucidate the reason for the key feature, i.e., the clearly defined stability of the polyplexes formed by supercharged polyamines. The main findings of the experimental study were confirmed by the results of full atomic modeling, and the principal regularities responsible for the structure, stability, and properties of the supercharged polyplexes have been elucidated for the first time.