Soil microbial flora is usually used as a biomarker of sustainability of farmland. With the research on soil microbiology gradually maturing, it becomes advisable to evaluate farmland quality from the angle of soil microbiology and to analyze whether or not the tract of farmland under study may have a bright future of sustainable development from the aspect of soil microcosmic mechanisms. However, the farmland quality evaluation systems, currently available, have not yet illustrated how to evaluate farmland quality from the angle of soil microbiota. Based on reviews of the literature concerning farmland quality and soil microbiology, this paper elaborated how to use soil microbiota as feedback of farmland quality, especially when related to farmland management, food production and soil pollution. In line with the existing international and domestic standards of the industry, the paper marked out microbial biomass , soil basal respiration, hydrolase activity and microbial diversity as, microbiological indices for the farmland quality evaluation systems. In using the common methods to evaluate soil quality, the objects studied are always kept in a stable state. Moreover, the evaluations using these methods seldom involves any soil microbial indices. They usually need the support of basic data or are more suitable for analysis of large-scale soil properties and positioning. In addition, most of the evaluation methods are more suitable for scientific research, but not so for application to farmland improvement projects. Based on the designing of ecological comparative experiments and the method of Duncan test, a new flowchart was plotted out for farmland quality environment. By comparing control with treatment in the experiment, variance rate and variation value could be obtained for analysis of effect of the treatment. Post hoc validation tests, were performed to analyze significance of difference between treatments and control. In the end, an effect-evaluation table was established, reflecting effects of treatments on farmland quality. This study indicates that the farmland quality evaluation system encompassing soil microbial indices is more sensitive and comprehensive than the traditional ones, and the combination of soil microbial properties and soil physico-chemical properties makes the environment more reliable. It is worth to note that the new system is more suitable for quantitative indices, and needs to analyze results of the evaluation by taking into account changes in soil physical and chemical properties. For the relative abundances of soil microbial communities obtained via sequencing, this method still has certain points worth pondering over. It is advisable to adopt the method of community classification in analyzing soil microbial communities. Soil microbial properties readily reveals mechanism of changes in farmland. Even though in the course of using soil microbiota to evaluate farmland quality, there are still a lot technical and analytical difficulties to overcome, it cannot be ignored that soil microorganisms play an irreplaceable role in the evaluation of farmland quality and will become an important analytical tool for defining quality of farmland in future.