In order to explore the influence of different water quality control methods on the number of heterotrophic bacteria and vibrio in the bottom mud of sea cucumber farming ponds, three types of sea cucumber farming ponds, namely sea cucumber farming ponds under natural tide management (hereinafter referred to as natural ponds), sea cucumber farming ponds equipped with microporous aeration aerators (hereinafter referred to as microporous aeration ponds) and sea cucumber farming ponds equipped with water quality regulator ponds (hereinafter referred to as water quality regulator ponds) were selected. The annual changes in the number of heterotrophic bacteria and vibrio in the bottom mud of sea cucumber farming ponds were detected. The results showed that the number of heterotrophic bacteria in the bottom mud of sea cucumber cultivation ponds was 94 400-377 625 cfu/g in natural ponds, 62 633-247 309 cfu/g in microporous aeration ponds, and 115 037-273 071 cfu/g in water quality regulator ponds, of which natural ponds are highest in January and lowest in March, microporous aerated ponds are highest in May and lowest in June, and water quality regulator ponds are highest in April and lowest in August. The number of vibrio in the bottom mud in the sea cucumber culture ponds was 0-3 291 cfu/g in natural ponds, 35-5 412 cfu/g in microporous aeration ponds, and 0-3 037 cfu/g in water quality regulator ponds. All sea cucumber farming ponds showed the characteristics of "highest in spring and the lowest in winter". The ratio of vibrio to heterotrophic bacteria was relatively higher in April and May, and lower in February. Preliminary experiments are conducted to compare the effects of different water quality control methods on the number of microorganisms in the bottom of sea cucumber farming ponds, and provide a theoretical basis for improving the bottom quality of sea cucumber farming ponds and exploring microbial changes.