Development of rapid and powerful mutagenesis and high throughput adaptive evolution tools is of importance for breeding of microbes aiming at application in environmental and industrial biotechnology. ARTP (atmospheric and room temperature plasma) mutagenesis system developed by our group can directly cause complex and diverse genome mutation including chain break and bases mutation via a unique mechanism. ARTP has the strongest DNA damage, and the highest mutation rate among the physical and chemical mutagenesis methods. Mechanistic study and practical application demonstrated that ARTP mutagenesis is a powerful tool for microbial evolution engineering to create diverse phenotypes. For developing an integrated platform capable of combing ARTP mutagenesis and high throughput adaptive evolution, we further developed a microdroplet-based microbial culture (MMC) system which can be operated automatically with high throughput culture on microchips, good repeatability, online detection of growth states, reprogrammable software, automatic addition of gradient chemical factors. The ARTP mutagenesis together with MMC system is an enabling platform for breeding of diverse microbes, especially aiming at application in open systems, such as environmental biotechnology and bioenergy, which require non-GM microorganisms.