The invention belongs to the field of microbe fertilizers, and provides a micro-ecological composite inoculant special for overcoming watermelon continuous cropping obstacle and an application method so as to solve the problems that various method for overcoming watermelon continuous cropping obstacle possess responding defects. The inoculant is prepared by mixing bacillus laterosporus, bacillus amyloliquefaciens, bacillus circulans, propionibacterium shermanil, tree microbacterium sp., bacillus laevolacticus, trichoderma harzianum, trichoderma asperellum, trichoderma fasciculatum Bissett, paecilomyces lilacinus, streptomyces syringini, gordonia sp., tsukamurella sp. and conexibacter sp. according to a certain ratio. The composite inoculant guarantees watermelon quality safety and environment zero pollution, and helps to reduce peasant production cost, guarantee agricultural product quality safety and protect ecological environment. The composite inoculant effectively overcomes watermelon continuous cropping obstacle, and watermelon which is truly nuisance-free, pure in mouthfeel and high in sweetness is produced. The composite inoculant possesses significant meaning on watermelon production, watermelon peasant income increase, consumer health guarantee, environment pollution reduction and maintenance of agricultural sustainable development.