Abstract: 【Objective】To screen dominant microorganisms in root of papaya with strong lodging resistance，and to mine key genes of differential expression of papaya lodging resistance，so as to provide reference for revealing mechanism of papaya lodging resistance and related variety breeding selection.【Method】In the experiment，three treatments were set up，conventional fertilizer application（2.5 kg organic fertilizer per plant，CK），fertilizer deficiency treatment （no organic fertilizer， WLR）and high organic fertilizer treatment（10 kg organic fertilizer per plant，SLR）. Based on transcriptome and rhizosphere microorganism data，association analyses of weighted gene co-expression network analysis （WGCNA）were conducted to analyze key genes related to papaya lodging resistance and changes of rhizosphere microorganisms.【Result】 The plants treated with SLR had the strongest lodging resistance，followed by CK，and the plants treated with WLR had the worst lodging resistance. The plant height，internode length，and stem diameter of WLR treated plants were significantly lower than those of CK and SLR treated plants（P<0.05）. Through microbiome data analysis，dominant microorganisms that affected the trait of lodging resistance were identified：Streptomyces，Bradyrhizobium，RB41 and Chitinophaga. Two modules related to papaya lodging resistance（royal blue module and light yellow module）were obtained through WGCNA analysis. Weighted gene co-expression networks based on these two modules were established and then 6 core genes possibly related to papaya lodging resistance were screened： acetyl-CoA acetyltransferase（AACT）， polyadenylate-binding protein RBP47-like gene（RBP47），mitochondrial import inner membrane translocase subunit gene（TIM9），Calcium dependent channel 7TM region gene（HYP1），phloem protein filament network protein gene （SEO），and cysteine proteinase inhibitor a-like gene（CPI）. Functional analysis of the core genes showed that the royal blue module was involved in papaya terpenoid metabolism regulation，while the light yellow module was involved in papaya phloem growth regulation.【Conclusion】 Dominant rhizosphere microorganisms are closely related to papaya lodging resistance，and as they can strengthen lodging resistance through regulating papaya stem growth，they can be taken as one of the microorganism screening markers for highly lodging-resistant papaya breeding.