This paper deals with intramolecular spin alignment in organic high-spin molecules and focus especially on a large negative spin polarization induced by pi-topology. Utilizing a topological connectivity of pi-electron network, spin inverted moiety with large negative spin densities can be realized in organic high-spin molecules, which are models of polymer-based ferrimagnets. As an example, two different organic high-spin molecules, 3,4’-diphenylmethylenbis(phenylmethylene) and 4-(diphenylmethylene)-4’-(m-phenylenbis(phenylmethylene))-ether, have been investigated. In order to clarify the electronic structure, the spin density distributions have been determined by single-crystal ESR and ENDOR experiments. The analysis of the H-1- and C-13-hyperfine tensors gives a clear evidence of the large negative spin polarization. The spin alignment in these molecules is discussed in terms of the VB picture based on a generalized Hubbard model.