A variety of physical, chemical and biological methods have been used to synthesize nanoparticles in which biological methods are green chemistry approachs, interconnecting organism with nanotechnology. Microorganisms are an important group of organism which can be used in nanoparticles synthesis, because they are growing fast, easy to culture, inexpensive and widely available. The diversity of microorganisms and nanomaterials determines the diversification of its synthetic mechanism. According to researches of home and abroad, this paper focus on summarizing mechanism of synthesis nanoparticles using microorganisms. The prospects of biosynthesis nanoparticles using microorganism have also been addressed.