An isopropanol-based Gemini quaternary salt (GC-S) with organic counterion was synthesized from dodecyl dimethyl tertiary amine, epichlorohydrin and p-toluenesulfonic acid. The synthesis process was optimized by orthogonal experimental. The products were characterized by FTIR , 1HNMR and ESI-MS, which demonstrated the successful synthesis of the expected structures. GC-S had a high surface activity with a cmc of 24.06 mN/m and a CMC of 2.09×10-4 mol/L. GC-S was compared with conventional Gemini quaternary ammonium salt with chloride as counterions (GC-Cl) and single-chain quaternary ammonium salt (1231). The results indicated that GC-S had better wettability because of the shortest sink time (175.2 s) for canvas swabs in aqueous solution. GC-S showed better foaming and foam stabilization performance due to larger starting foam volume (390 mL) and smaller defoaming volume (20 mL). GC-S displayed better emulsification performance because the partition out the quantitative aqueous layer from the emulsification system of aqueous solutions with liquid paraffin needed a larger time (317 s). GC-S (10 mg/kg) showed very high antibacterial activity against both E. coli and Staphylococcus aureus.