Excessive input of nitrogenous fertilizer not only wastes resources but also pollutes environment. Seasonal withdrawal of nitrogenous fertilizer is a practical method to reduce application rate of the fertilizer in Taicang. This paper compares this practice with the traditional one in soil microbe population and functional diversity index of the microbe at the community level. The results showed that no significant difference was found in populations of bacteria, fungi and actinomyce between the two fertilization modes. BIOLOG analysis indicated that no significant difference was observed either in value of Average Well Color Development (AWCD), Shannon diversity index and Simpson diversity index between the two. There were 3 principal component factors (PCF), screened out of 95 factors by Principal Component Analysis (PCA). Although PCF 2 showed some difference between the two, but PCF 1 and 3 did not. All of the above imply that short-term seasonal withdrawal of nitrogenous fertilizer has no significant effect on soil microbe in population and only a little in functional diversity.