An efficient and rapid synthesis of carbohydrate derivatives was accomplished using a chaotic microreactor. The reactor shaped as split-and-recombine (SAR) structure which combines mixing mechanisms of both multi-lamination (diffusion) and chaotic advection to enhance mixing and reaction. Using two steps reaction process in SAR-microreactors, the carbohydrate derivatives, aldo-naphthimidazoles were generated by linkage of naphthalenediamine with mono-, di- or trialdoses in less than 10 s with satisfactory yield. The SAR-microreactor completes the process required just seconds (0.1–10 s), which was about 10 −3–10 −6 the duration for the macro flask. Within the same duration, the yield of the product formed from SAR-microreactors was also much enhanced than the T-shaped microreactors. The SAR-microreactor has a superiority to enable other chemical reactions quickly and economically.