The microbiology was introduced in foundation treatment. Several Carbonatemineralization microorganisms and polysaccharides viscose microorganisms were screened and the microorganisms No.ATCC 6453，3，polysaccharides viscose microorganisms 5 and 6 were used in silt modification. The engineering properties of silt before and after modification were compared by unconfined compressive strength test and indoor seepage test. The microstructures of silt incorporating different microorganisms were analysed by mean of scanning electron microscope and energy dispersive Xray (EDX) analysis. And the modification mechanism of silt has been revealed. These studies indicate that certain engineering properties of silt can be improved by incorporating microorganisms.