[Objective] This papar was about the effects of a kind of probiotics on several kinds of biological factors in seawater ponds. The probiotics was independently researched and developed by our research team. The main components of the probiotics were Bacillus sp. and Pseudomonas sp.. The biological factors included three kinds of breeding living being and the microorganism and the plankton. The objective of this study was for establishing technical system of ecological control of microorganisms. The research methods were described below. [Methods] During the experiment, the probiotic was spilled in the experimental ponds every 15 days. The density of heterotrophic bacteria and vibrio of the water and sediment were measured at the end of the month. The species and density of plankton was investigated at the end of the month. The growth rate and survival rate of cultured organisms was measured by the end of harvest season. The experiment was carried out nearly three months. [Results] There were three results. Firstly, the probiotics could enhance the growth and survival rate of two kinds of breeding living being, including Litopenaeus vannamei and Portunus trituberculatus. The survival rate and growth rate of the Litopenaeus vannamei of test groups enhanced respectively 11.3% and 1 400% compared with the control groups. The survival rate and growth rate of the portunus trituberculatus of test groups enhanced respectively 1.2% and 37.5% compared with the control groups. Secondly, the probiotics could enhance the density of heterotrophic bacteria, and restrained the growth of vibrios. The heterotrophic bacteria density of test groups in the water was higher 58.5% than the control groups. The heterotrophic bacteria density of test groups in the sediment was higher 58.5% than the control ponds. The vibrios density of test groups in the water was lower 39.7% than control groups. Thirdly, the probiotics could improve the density of Chlorophyta algae and Bacillariophyta algae, and inhibited the growth of Cyanophyta algae and Pyrrophyta algae. [Conclusion] It came to the conclusion that the probiotics could effectively improve biology community structure and the growth rate of some farmed species in the aquaculture ponds.