The study on soil enzyme activities under wheat-rice rotation system of 25a long-term site-specific experimental fields of paddy soil in Taihu region shows: there was no obvious regularity for the activity variation of five types of soil enzymes under different fertilization treatments in wheat system; there were no significant differences among most soil enzyme activities under different fertilization treatments in rice system. Paired-samples comparison shows that there were no significant differences among most soil enzyme activities under the same fertilization treatments under wheat-rice rotation system, only acid phosphatase activity under rice system of the treatment of NPK fertilizers + stable manure was significant higher than under wheat system. The reasons for no significant differences among most soil enzyme activities might be attributed to the saturation of soil enzymes from accumulation by 25a long-term site-specific fertilization, thus, they won’t show significant responses to the ectogenic fertilizers.