Paenibacillus polymyxa NBmelon-1 is a highly effective biocontrol bacterial strain isolated from melon roots. To study the genetic information of P. polymyxa NBmelon-1 and investigate its biocontrol mechanisms, the whole genome of strain NBmelon-1 was sequenced using the third-generation PacBio sequencing technique, and the genome was used to mine potential functional genes for biosynthesis of the secondary metabolites. Validation was carried out by detecting expression of the genes related to antifungal activity and plant-growth promotion and testing the antifungal activity of the crude extracts. The results showed that the genome size of P. polymyxa NBmelon-1 was 5.7 Mb with the GC content of 45.68%, harboring 4,984 coding genes. The genome contained genes related to induction of plant resistance and promotion of plant growth as well as the genes for hydrolases. A total of five gene clusters for biosynthesis of lipopeptide metabolites were predicted, including those for polymyxin, fusaricidin B, tridecaptin M, tridecaptin and peanilipoheptin. Crude extract was obtained from the cultures of NBmelon-1 using the acid precipitation method, and it showed a significant inhibitory effect on growth of a variety of pathogenic fungi from melon. The growth-promoting potential test showed that the bacterial strain was able to synthesize the phytohormone IAA, to produce iron carriers, and to provide nitrogen to plants. In conclusion,?P. polymyxa?NBmelon-1 has good prospects for agricultural applications.