Sea cucumber (Apostichopus japonicus) farming industry has been developing rapidly in North China, but at the meanwhile sea cucumber diseases has become a growing problem. The environmental deterioration was considered one of the main causes. A type of sediment improver studied by our research group has been proved to be effective in adjusting the sediment environment of the sea cucumber culture ponds. In order to detect the responses of the bacterial community to the sediment improver, we conducted experiments using the sediment from the disease-occurring sea cucumber culture ponds. The sample treated with the sediment improver was the trial group and that without the improver was the control group, and we set 3 parallels for each group. The plant counting method and the most probable number method were used to determine the change in the numbers of several bacterial groups in the sediment after the addition of the sediment improver. The bacterial diversity was analyzed using the 16S rRNA gene PCR-DGGE and the sequencing techniques. The results showed that in the trial group the numbers of the heterotrophic bacteria, the nitrifying bacteria and the sulfate- reducing bacteria in sea cucumber pond sediments increased in the first 2 to 4 days, followed by a decrease and then maintained at a low level, and the increase was significantly smaller than that in the control group. The numbers of Vibriols and sulfurizing bacteria sharply declined 1 day after the addition of the sediment improver, which were significantly lower than those in the control group. The sequencing result of DGGE bands showed that the dominant bacteria in the sea cucumber culture environment belonged to chloroflexi, moraxellaceae, Caulobacteraceae, Aeromonadaceae in proteobacteria, bacillaceae, and lactobacillaceaein in firmicutes. The bacterial diversity indexes varied between 2.5 and 3.5. The numbers of 2 species of Aeromonus were observed to decline after the addition of the sediment improver in the trial group. Therefore, we concluded that the sediment improver could adjust the numbers of different bacterial groups in the sediment environment and reduce the quantity of some pathogenic bacteria. The sediment improver may thus improve the quality of the pond sediment environment and protect A. japonicus from diseases.