Soil biotic communities play vital roles in enhancing soil nutrient cycling and soil fertility.  Long-term excessive nitrogen (N) application is disadvantageous to the stability of soil food webs and affects arable soil health and sustainable utilization.  Proper organic substitution is essential to improve soil health and alleviate the disadvantages of excessive chemical fertilization.  However, the biological effects of various organic amendments on soil micro-food webs are poorly understood.  In order to explore the effects of various organic amendments including stover, biochar and manure on soil micro-food webs (microbial and nematode communities), a field plot experiment with maize having five treatments viz., 100% urea (100% N), 70% urea (70% N), 70% urea plus stover (Stover), 70% urea plus cattle manure (Manure) and 70% urea plus biochar (Biochar) was conducted.  Manure treatment increased the carbon (C) to N use efficiency of soil microbes, which contributed to the retention of soil C, while Biochar treatment elevated soil organic C (SOC) and soil pH.  Additionally, Biochar treatment mitigated the negative effects of soil acidification on the soil micro-food web and reduced the abundance of plant parasites.  Overall, the biological effect of organic amendments was distinguished from chemical fertilization (100% N and 70% N) through principal co-ordinates analysis.  Negative relationships among soil properties, microbial and nematode biomass in the 100% N treatment were diminished in treatments where chemical fertilizer was reduced.  The bottom-up effects on soil food webs were observed in organic substitution treatments.  In conclusion, organic amendments improved soil fertility by regulating soil microbial and nematode communities in the cropland ecosystem, alleviated the negative effects of chemical fertilizer on the micro-food webs and controlled the trophic cascades among soil biota.