Zigzag micro-channel reactors have been fabricated and used for continuous alkali-catalyzed biodiesel synthesis. The influences of the main geometric parameters on the performance of the micro-channel reactors were experimentally studied. It has been found that the zigzag micro-channel reactor with smaller channel size and more turns produces smaller droplets which result in higher efficiency of biodiesel synthesis. Compared to conventional stirred reactors, the time for high methyl ester conversion can be shortened significantly with the methyl ester yield of 99.5% at the residence time of only 28 s by using the optimized zigzag micro-channel reactor, which also exhibits less energy consumption for the same amount of biodiesel during biodiesel synthesis. The results indicate that zigzag micro-channel reactors can be designed as compact and mini-fuel processing plant for distributive applications.