Changes of microbe and organic matter content in paddy soil applied with straw, manure and nitrogen fertilizer were analyzed. Experimental plots in the rotations had 10 treatments, i. e. with or without straw, manure, nitrogen fertilizer and a control. The amount of straw was zero or 6000 kg/hm2, that of manure was zero, 1500 kg/hm2, 3000 kg/hm2, 4500 kg/hm2, or 6000 kg/hm2, that of nitrogen fertilizer was zero, 240 kg/hm2, 270 kg/hm2, 280 kg/hm2, 285 kg/hm2, 300 kg/hm2, or 330 kg/hm2. The results showed that with the range of nitrogen fertilizer application of 0-330 kg/hm2, increasing nitrogen fertilizer could promote the decomposition of straw at the situation of straw amending into soil. Each measure of straw, manure and nitrogen fertilizer could increase the bacteria, the fungus, ray fungi quantity in soil in some degree. The synthesis applying with straw, manure and nitrogen fertilizer could coordinate increase microbe quantity in soil, enhance the soil biomass nitrogen and organic matter content, and when the quantity of straw was 6000 kg/hm2, the quantity of manure was 4500 kg/hm2, the quantity of nitrogen fertilizer was 240 kg/hm2, the effects were better. It indicated that a good amount of manure and nitrogen fertilizer could increase soil microbial numbers and organic matter content in straw amended agro-ecosystem, which was very important in improving soil fertilization.