In a pot experiment, soybean plants were irrigated with the second grade and third grade reclaimed water to study the changes of physicochemical properties and the microorganism groups in root zone of soybean. The results indicated that irrigation with reclaimed water improved soil fertility, and contents of organic mater and available phosphorus increased markedly. Compared with the control without irrigation with reclaimed water or irrigated with fresh water, the contents of heavy metals lead (Pb) and cadmium (Cd) in soil had no significant accumulation, but the electric conductivity (EC) of the soil increased significantly which resulted in the increased of salinity to a certain extent. Irrigation with reclaimed water enhanced the bacteria and Actinomyces amounts while the fungi amount was not enhanced. The difference in number of Actinomyces between irrigation with second grade reclaimed water and the third reclaimed water was obviously and higher than that of control of fresh water irrigation. Irrigation with reclaimed water increased the urease activity in root zone of soybean, and the alkaline phosphatase activity was the highest. The soil microbe number and enzyme activities were significantly correlated with soil nutrients, so they could be used as the indexes to evaluate the fertility and environment quality of soil.