Fatty acid methyl ester sulfonate (MES) is an environmentally friendly anionic surfactant. It contains RCH(CO2Me)SO3Na (α-MES) as the active component and RCH(CO2Na)SO3Na (the disodium salt) whose content must be lower than 5%. In this paper, MES was prepared first in a falling film microreactor (FFMR) by sulfonation of hydrogenated palm oil methyl ester (ME) with SO3 diluted with N2, followed by aging in a tubular reactor and subsequent bleaching and neutralization with NaOH. The influences of the ME flow rate, the channel size, the N2 flow rate, the SO3-to-ME molar ratio, and the sulfonation temperature in the sulfonation step, as well as the influences of the SO3-to-ME molar ratio, the aging residence time, and the aging temperature in the aging step, were all examined. The results indicated that the ME flow rate had no evident influence on the ME conversion and the α-MES concentration both without overflow and with overflow. In the sulfonation step, the disodium salt (disalt) concentration increased with increase in the ME flow rate, the channel size, the SO3-to-ME molar ratio, and the sulfonation temperature or decrease in the N2 flow rate. In the aging step, the ME conversion, the α-MES concentration, and the disalt concentration increased with increase in the SO3-to-ME molar ratio, the aging residence time, and the aging temperature. The results of 1H NMR spectra indicated that RCH(CO2Me)SO3H was mainly formed in the sulfonation step in the microreactor, while it was formed in the aging step when the sulfonation was carried out in the conventional falling film reactor. Accordingly, a sulfonation reaction mechanism in the FFMR different from that in the conventional FFR was proposed. The final products with an α-MES concentration of 86.3% and a disalt concentration of 1.2% were obtained under the conditions of a ME flow rate of 2 mL/min, a channel size of 300 × 100 μm, a SO3-to-ME molar ratio of 1.2, a N2 flow rate of 900 mL/min, a sulfonation temperature of 85 °C, an aging temperature of 90 °C, and an aging residence time of 19.7 min.