[Objective] The use of organic manure as alternative for chemical fertilizer has been recommended as an effective method to mitigate impacts of chemical fertilizer on the agricultural system and improve soil fertility. However, how soil microbial communities respond to the organic input following fertilizer reduction remains poorly understood.[Method] In the current study, the technique of Illumina MiSeq sequencing combined with the construction of molecular ecological networks was used to investigate community composition and structure of the molecular ecological network of the soil bacteria and fungi in the field of fluvo-aquic soil under a wheat-maize rotation system. Furthermore, correlation networks between soil organic manure (SOM) content and bacterial and fungal communities were constructed. The fertilization regimes were designed as follows:conventional chemical fertilizer (NPK), reduced chemical fertilizer (NPKR), chemical fertilizer partly substituted with straw (NPKRS), chemical fertilizer partly substituted with organic manure (NPKRO), chemical fertilizer partly substituted with organic manure and straw (NPKROS).[Result] Results show that chemical fertilizer reduction and organic substitution significantly increased the content of soil SOM. In the case of bacterial community ecological network, compared with Treatment NPK, the treatments of chemical fertilizer reduction and organic substitution increased the numbers of network nodes and edges, but reduced the average path length. Treatments NPKRS and NPKROS were higher than the other three treatments in average clustering coefficient and the network density. With respective to fungal ecological network, Treatment NPKR increased the numbers of network nodes and edges, while the organic substitution treatments increased the average path length and reduced the average clustering coefficient, as compared to Treatment NPK. Treatment NPKR was the highest in network density among all treatments, but the lowest in modularity. Compared with Treatment NPK, all the other treatments increased the proportion of bacterial flora that were significantly and positively related to soil SOM content, but decreased the proportion of fungal flora that were significantly and negatively related to soil SOM content. Some flora, like Proteobacteria, Chloroflexi, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes and Acidobacteria, play an important role in the soil bacterial molecular ecological network, while some, like Ascomycota, Basidiomycota and Glomeromycota, do a significant one in the soil fungal molecular ecological network.[Conclusion] In conclusion, partial substitution of chemical fertilizer with organic manure or material increases the bacterial molecular ecological network in size, while simultaneously improving the transferring efficiency of substances, energy and information among species. The substitution with straw enhances interaction between bacterial communities and makes the bacterial community more sensitive to disturbance of the external environmental factors. The reduction of chemical fertilizer increases the fungal molecular ecological network in size and community interaction, and the substitution with organic manure or material improves stability of the fungal community structure.