Paenibacillus polymyxa NBmelon-1 is an efficient biocontrol bacterium isolated from the roots of sweet melons. The third-generation of PacBio sequencing technique was used to sequence the whole genome of strain NBmelon-1 to study the biocontrol mechanisms of P. polymyxa NBmelon-1. The potential functional genes were analyzed and clusters of genes involved in the synthesis of secondary metabolites were predicted. The expression of genes related with antibacterial effect and promoting the growth of plants was detected. The antagonism test of crude extracts was used to identify the main components of antibacterial substances and validate the potential of the bacteria to promote the growth of plants， further clarifying its biocontrol mechanism. The results showed that the genome of P. polymyxa NBmelon-1 was 5.7 Mb， with a GC content of 45.68% and 4 984 coding genes. There were a large number of genes involved in inducing plant disease resistance， hydrolytic enzymes， and promoting plant the growth of plants in the genome. A total of five clusters of genes involved in the synthesis of secondary metabolites of lipopeptides were predicted. The crude extracts isolated from NBmelon-1 culture with acid precipitation method had significant antibacterial activity against a variety of pathogenic fungi from melon， indicating the presence of antibacterial substances. The results of growth potential test showed that the strain was capable of synthesizing growth hormone IAA， producing iron carriers， and providing nitrogen elements for plants. It is indicated that P. polymyxa NBmelon-1 is a multifunctional biocontrol bacterium with broad prospects for development and application in agricultural production.