Abstract During the anomalously hot summer of 2018, the water temperature in a sea cucumber culture pond reached 28–33 °C. As a result, many sea cucumbers died from the high temperature, causing huge economic losses. Currently, changes in the bacterial community of the sea cucumber culture pond ecosystem during high temperature remain largely unknown. In this study, we investigated the effects of high temperature on the community composition and function of the sea cucumber culture pond ecosystem using high-throughput sequencing. The results showed that bacterial communities in the Apostichopus japonicus intestine, surrounding water and sediment responded quickly to high temperature, as indicated by an obvious succession process of the dominant and specific bacterial community. At high temperature, the richness and diversity of the bacterial community in the water and sediment decreased significantly (P