In the previous studies, gemini lipoamino acids (GLAA) were always synthesized by complex multistep organic synthesis, which involved a large number of byproducts and organic solvents. To develop a straightforward, efficient, and renewable synthesis strategy for GLAA, in this study, a type of novel green solvents, natural deep eutectic solvents (NADESs), were adopted as the solvents for these reactions. Five commercial enzymes were involved in the enzyme screening section, and lipase B (CALB) tended to have the best performance in NADESs systems. The optimization procedure was performed using the Taguchi crossed array method and the highest yield of GLAA (59.14 ± 0.51%) was obtained in choline chloride-glycerol (C-Gly). The purification procedure was carried out with ethyl acetate and water, and the isolate yield ranged from 86.31 ± 2.36 to 91.34 ± 2.26%. With 10 times recycling, the yield of GLAA in C-Gly decreased from 59.14 ± 0.51 to 51.31 ± 0.68%. Interestingly, a synergistic effect of CALB and NADESs was found in the enzymatic synthesis of GLAA, which can be attributed to fatty acids being activated by chloride ions via hydrogen-bonding interactions and resulting in an enhancement in its electron-attracting ability.