High temperature and rainy weather bring many challenges such as frequent occurrences of pests and diseases to tropical agriculture. At present, microorganisms such as Trichoderma, Bacillus and Streptomyces have been widely used to ensure sustainable and environmentally friendly production of tropical agriculture, and the combination of different functional microorganisms has greater potential as plant growth promoters and biological control agents. In this paper, the application of several types of common microorganisms and their products in the development of tropical sustainable agriculture was reviewed. The mechanisms of functional microorganisms were summarized, including direct mechanisms such as hyperparasitism and antibiotic production, and indirect mechanisms such as competition for space and nutrients, activation of host plant defense ability and modification of rhizosphere microflora. The future research directions and hotspots of microorganism consortia in agricultural production and applications were prospected.