The deep scattering layer (DSL) is crucial for marine ecosystems and oceanographic studies. It consists of dense aggregations of organisms such as zooplankton and micronekton, which form a key link in the food web, transferring energy from primary producers to higher trophic levels. Understanding the DSL is essential for assessing ecosystem health, global biogeochemical cycles, and the effects of climate change on ocean dynamics. Based on the acoustic data from October 2012 to July 2020 in the southwestern Indian Ocean, hotspot analysis and maximum entropy model were used to study the potential habitats’ distribution on hotspots of deep scattering layers under different IODs. The results showed that the maximum entropy model had a good performance with the accuracy of the model was more significant than 0.9. Dissolved oxygen had the highest contribution rate to habitat distribution, and the average contribution rate was 50.88%. The gravity centre of DSL hotspot habitats mainly moved in the northwest to southeast direction, and the most significant changes were observed during the first cold phase of IOD. DSL hotspot habitat was distributed between 30 °-45 ° S and 11-22 °C isotherms, which indicated a specific latitude correlation. This research showed that the suitable habitat changes on DSL hotspots were influenced by dissolved oxygen. The maximum entropy model could effectively predict the distribution of DSL hotspots' habitats. This study can provide new references for elucidating the spatial distribution and resource variation patterns of DSL.