Microbial agents especially those composed by a variety of microorganisms with different degradation functions and symbiotic relationship in an appropriate ratio or prepared by mixed culture were an important researching area in applied microbiology recently, which accomplish transforming scientific theories into practical productive forces. Microbial agents have been gradually used in some aspects of ecological engineering to regulate the ecological balance and protect the environment, such as planting, breeding and pollutant treatment, and have achieved good results, especially in environmental protection. Their significant advantages have been widely recognized. Using microorganisms to solve environmental pollution has a good prospect, that is why more and more people are committed to the research and development of microbial agents. Since 1970, some products of complex microbial agents were developed in Europe, America and Japan, and were started large scale productions. The microbial agents were firstly applied to treating sewage, industrial wastewater, and other chemical pollutions. In this paper, the applying scope, effects and mechanism of microbial agents in the field of ecological engineering were summarized, from international and domestic literatures. The strains breeding methods and several types of bacteria commonly used in the development of microbial agents are summed up. And the effects of wastewater treating projects of through applying lactic acid bacteria, yeast, photosynthetic bacteria, bacillus were introduced through some examples. Meanwhile, mixed microbial culture and the interacting mechanisms in the study of microbial agents were discussed. Many studies showed that the degradation or transform of organic matters needs cooperation by varies types of microorganisms, and the complex biological and chemical interaction could not be completed by single category microorganism. We pointed out that the current researches on microbial agents are mostly focused on the effect of application, but few of the current researches was related to the molecules of mechanism, which was demonstrated the mutual interaction of different microbial strains. In future researches, the internal degradation and synergistic reaction should be developed, and the detail affecting objectives in different habitat of microbial agents should be determined. When the synergistic and anticatalystic mechanisms of complex microbial agents were clearly demonstrated in the aspects of microbial physiology and metabolism, the technology of mixed cultivation could be promoted, and the selection of microbial agents groups could optimized, and the degrading functions of microbial agents could be best developed. In the future, people will pay more attention to the quality of environment, the safe and efficient microbial agents will increasingly be welcomed. With the continuous development of science and technology, microbial mixed culture techniques and the efficiency of microbial agents will keep improving, and the range of application will more and more extensive. Maybe it can become a kind of daily necessities and replace some cleaning products we use now, which can largely reduce environmental pollution.