Biobutanol can be indigenously synthesized by solventogenic Clostridium species; however, these microorganisms possess inferior capability of utilizing abundant and renewable organic wastes, such as starch, lignocellulose, and even syngas. The common strategy to achieve direct butanol production from these organic wastes is through genetic modification of wild-type strains. However, due to the complex of butanol synthetic and hydrolytic enzymes expression systems, the recombinants show unsatisfactory results. Recently, setting up microbial co-culturing systems became more attractive, as they could not only perform more complicated tasks, but also endure changeable environments. Hence, this mini-review comprehensively summarized the state-of-the-art biobutanol production from different substrates by using microbial co-culturing systems. Furthermore, strategies regarding establishment principles of microbial co-culturing systems were also analyzed and compared.