Sea cucumber is an important species cultivated in seawater ponds in Liaoning and Shandong provinces of China in the past 30 years. However, the current conventional techniques for improving pond water quality, such as water exchange by spring tides (WEST) and submerged aerator (SA), are not very ideal. The ponds can still form thermohaloclines in February and June, and a large number of macroalgae will be produced in summer and autumn. Jet Water Mixer (JWM) is a new water quality control device for sea cucumber pond. In order to explore the effect and mechanism of water quality improvement of sea cucumber breeding pond by JWM, we measured the annual changes of water quality and the changes of bacterial flora and function in spring and autumn by 16SrRNA high-throughput sequencing technology under the three water quality control methods. Nine adjacent ponds of the same size and shape were selected for the experiment. Three ponds with JWM were used as the experimental group, and the other six ponds were used as the control group, among which 3 ponds were used as SA control group and 3 ponds were used as WEST control group. The results showed that the contents of NH4+-N, NO2--N and NO3--N in the pond water with JWM were decreased, and the contents of O2, PO43--P, TN, TP, chlorophyll and suspended matter were increased, But except that the content of chlorophyll in the pond water with JWM was significantly higher than that in the control pond, there was no significant difference in other water quality indexes. The effect of water quality regulation on the composition of dominant bacterial groups in pond water showed that the higher the classification level, the smaller the effect, while the lower the classification level, the greater the effect. The composition of the top 10 dominant phyla and the top 3 dominant classes in the pond water with JWM were basically the same as that in the control ponds. The first and second dominant phyla are Proteobacteria and Bacteroidetes. The first three dominant classes were Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria, but the composition of the dominant genus varied greatly in different ponds. Lefse analysis showed that JWM significantly increased the abundance of Firmicutes-Bacilli-Lactobacillales in the pond water (LDA SCORE > 4), and t-test showed that WEST significantly increased the abundance of Alteromonadaceae and SA significantly increased the abundance of Glaclecola in the pond water. FAPRTAX analysis showed that the main functional bacteria in each pond were chemoheterotrophy, aerobic chemoheterotrophy, sulfur oxidation, sulfur respiration, nitrate reduction, fermentation and plant pathogens. There was no significant difference in the annual mean abundance of the same functional bacteria among the ponds, but at the late stage of the experiment, there were large difference in the abundance of some functional bacteria between ponds. JWM increased the abundance of fermentation and plant pathogen bacteria and decreased the abundance of nitrate reduction bacteria. SA increased the abundance of nitrate reduction bacteria and decreased the abundance of plant pathogenic bacteria. The α-diversity of microbiota was the highest in the water of pond with JWM, and the lowest in that of pond with SA. The main environmental factors affecting the structure of bacterial flora were the contents of TP, NH4+-N and NO2--N in pond water. In conclusion, JWM significantly increased the abundance of Lactobacillales and plant pathogenic bacteria, and increased the α-diversity of bacterial flora in pond water. The former inhibited the growth of macroalgae, while the latter was beneficial to water quality stability.