To elucidate the antagonistic ability of polyethylene mulch applied in weed management of tea garden to the endophytic microbial community of tea plant root and common pathogens. In this study, 16S rRNA and ITS rDNA were used to analyze the diversity of microbial community structure in rhizosphere soil and root endophytic of tea plant under three different weeding methods: polyethylene mulching, hand weeding and no weeding (CK), and the isolation of endophytic bacteria in roots and the antagonism of pathogens. The results showed that the weeding methods had no significant effect on the rhizosphere and root endophytic microbial abundance, but the rhizosphere bacterial structure covered by polyethylene mulch was significantly different from that under hand weeding and CK, and the rhizosphere fungal diversity was also significantly higher than that of the other two groups. The community abundance of rhizosphere microorganisms Acidobacteria, Candidatus Rokubacteria and Aspergillus covered by polyethylene mulch decreased significantly. Bradyrhizobium, Solirubrobacterales and Alphaproteobacteria increased significantly. The abundance of bacteria Ktedonobacter, Reticulibacter, Ktedonosporobacter and Dictyobacter communities covered by polyethylene mulch was significantly changed, and the abundance of fungi Fusarium was significantly increased. Rhizosphere dominant bacteria were negatively correlated with soil available nitrogen content, while dominant fungi were significantly correlated with soil pH, total nitrogen and total potassium. Four antagonistic bacteria and eight antagonistic fungi were identified in root microbial isolation and antagonistic culture, respectively. The inhibition rate of Pseudomonas tolaasii, Aspergillus Aculeatinus, Penicillium Polonicum identified from the polyethylene mulch was 70.19% to 80.39% against the tea plants pathogen Pseudopestalotiopsis camelliae-sinensis and Fusarium oxysporum. The inhibition rate of Aspergillus piperis and Aspergillus brunneoviolaceus isolated from the CK was more than 80% against the pathogen Pseudopestalotiopsis camelliae-sinensis. This study provided a theoretical basis for the utilization of beneficial microorganisms in soil nutrient regulation and disease green control in tea garden by weed management and polyethylene mulch.