Developing a robust and facile process route for fatty acid methyl ester sulfonate (MES) synthesis is of importance for industrial applications. Herein, Taguchi orthogonal array (OA) approach was used for the first time to establish the optimum process condition for the sulfonation of methyl esters (ME) with chlorosulfonic acid (CSA). According to the experimental design, the most significant parameter was sulfonation temperature, followed by CSA/ME molar ratio. Under the optimum sulfonation conditions (that is, 70°C sulfonation temperature, 2.0 h sulfonation time, 1.5:1 mol/mol CSA/ME molar ratio and 2.0 h aging time), the MES yield and the corresponding signal/noise ratio were 92.08 ± 0.28% and 39.28, respectively. The obtained FTIR and 1H NMR data revealed spectra associated with methyl (CH2 asymmetric and CH2 symmetric stretching vibrations), esters (CO, CO, and OCH3), and sulfonate (SO) groups in the MES sample synthesized under optimal conditions, thus confirming the target MES product. Surface tension measurements revealed that the optimal MES sample had a low critical miscelle concentration of 0.082 g/L at a surface tension of 51.2 mN/m, implying the possibility of better performance.