Abstract We have recently proposed a new molecular design for neutral radical molecular conductors, based on the chemical composition of D2X-type charge-transfer salts (D = π-electron donor molecule, X = monovalent anion). Namely, we connected two tetrathiafulvalene (TTF)-based π-electron skeletons having a charge of +0.5 via a boron anion B–, to obtain a purely organic zwitterionic neutral radical {[(PDT-TTF-Cat)2]+B–}• that shows unique electronic states and properties in the crystal due to the intra- and intermolecular interactions of the +0.5-charged π-skeletons. In order to further explore the structural and electronic features of this kind of zwitterionic neutral radical conductor, in this study we have examined chemical modifications to {[(PDT-TTF-Cat)2]+B–}•. As a result, an analogue molecule {[(BMT-TTF-Cat)2]+B–}•, in which propylenedithio (PDT) groups on the TTF terminals in {[(PDT-TTF-Cat)2]+B–}• are replaced by bis(methylthio) (BMT) ones, was successfully synthesized as air-stable single crystals. Interestingly, this chemical modification causes intramolecular charge disproportionation between the two TTF-based π-skeletons (i.e., the monovalent cation radical TTF+• and the neutral TTF0) coupled to the modulation of the intermolecular distances and interactions between these π-skeletons, leading to electrical and magnetic properties significantly different from those of the crystal of {[(PDT-TTF-Cat)2]+B–}•.