A green strategy for the selective alkylation of cysteine-containing peptides in a continuous flow reactor has been developed, providing an efficient pathway to alkylated cysteine-containing peptides under mild conditions. This process does not need light, metal catalysts, or oxidative reagents. It provides a useful method for the modification of amino acids and peptides. As one of the low cost and synthetic versatile raw materials, the alkyl thianthenium salt can be used as an alkylation source in the preparation of alkylated cysteine-containing peptides. In addition, the microfluidics technology can shorten the reaction time and improve the efficiency, thus reducing the costs and energy consumption of the synthesis process. A series of alkylated cysteine-containing peptides (41 examples) has been synthesized here with a short residence time (14.0 min), and with good to excellent yields.