Six treatments including no fertilizer application (A),100% nitrogen fertilizer application (B),75%nitrogen and 25% peanut residue compost application(C),50% nitrogen and 50% peanut residue compost application (D),25% nitrogen and 75% peanut residue compost application (E),and 100% peanut residue compost application (F) were set. The endophytic bacterial diversity in rhizosphere soil and root system of tomato was analyzed with high-throughput sequencing. The effects of different ratios of nitrogen/peanut residue compost on rhizosphere soil and endophytic bacterial community structure in root system of tomato were studied to provide a theoretical basis for the balanced fertilization of tomato. The results showed that the composition of dominant soil bacteria at phylum level in rhizosphere was not changed,but their ratios were altered by application different fertilizers. The amount of dominant endophytic bacteria at phylum level in root of tomato was all decreased by only applying single nitrogen or peanut residue compost. At genus level,the composition and ratios of soil bacteria in rhizosphere and endophytic bacteria in root were altered by application of different fertilizers as well. Some dominant bacteria includingPseudomonas,Sphingobium,Pantoea and Klebsiella were disappeared under the treatment B or F,indicating that single application of nitrogen or peanut residue compost is not helpful to build a healthy rhizosphere soil microenvironment of tomato and improve plant resistance. Some pathogenic bacteria including Ralstonia were enriched as dominant endophytic bacteria in roots of tomatoes under single nitrogen or peanut residue compost treatment,indicating that soil health in rhizosphere and crop resilience is not improved by single application of nitrogen or peanut residue compost. 25% nitrogen and 75% peanut residue compost are the best combination for improving soil health in rhizosphere and crop resilience among the 6 treatments.