Cationic self-assembled monolayers (SAMs) composed of quaternary ammonium (QA) sulfur derivatives have been synthesized to control the distance between charged headgroups on gold substrates. Two molecules bearing resembling molecular structures, "gemini"-structured didodecyl dithiol (HS-gQA-SH) and didodecyl disulfide (QA-SS-QA), were utilized in this study, and the formation and structure of the SAMs were characterized by surface plasmon resonance spectroscopy (SPR), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared-reflection adsorption spectroscopy (FTIR-RAS). In the HS-gQA-SH SAM, the orientation and distance between QA groups are specified by the covalent bonding with ethylene spacer, while those of the QA-SS-QA SAM are determined by the electric repulsion between charged headgroups, that is, QA groups in the QA-SS-QA SAM are more randomly located, being more distant than with those in the HS-gQA-SH SAM. We found that L-tartaric acid, a probe molecule with two carboxyl groups having the distance of an ethylene unit, exhibits a strong affinity on the HS-gQA-SH SAM. In contrast, no specific binding was observed on the QA-SS-QA SAM. These results imply the possibility to build up a molecular recognition system on surfaces because of the control of the distance between the charged headgroups by using the gemini-structured molecular design.