<p>The Southern Ocean is a critical component in the Earth system by dominating the global heat and anthropogenic carbon uptake and supplying heat to melt the largest ice sheet. Variability and changes in the water masses of the Southern Ocean are thus important to the global energy and water cycles, carbon cycling, and sea-level change. In this article, we review the recent progress on understanding the variability and changes in the four major water masses in the Southern Ocean, including Subantarctic Mode Water, Antarctic Intermediate Water, Circumpolar Deep Water and Antarctic Bottom Water. Subantarctic Mode Water and Antarctic Intermediate Water show statistically significant strong circumpolar shoaling, warming, and density reductions since 1970s, indicating that signals of global warming have entered the interior ocean. Meanwhile, strong regional variability of Subantarctic Mode Water and Antarctic Intermediate Water responding to surface buoyancy forcing and westerly winds is attracting more attention. Circumpolar Deep Water is an important modulator of heat content and nutrient concentrations on continental shelves around Antarctica and has made significant contributions to the basal melting of Antarctic ice shelves. Since the late 1950s, a long-term freshening trend in Antarctic Bottom Water in the Ross Sea and its downstream region has been observed and is mainly attributed to the accelerated basal melting of ice shelves in West Antarctica. The shrinking of Antarctic Bottom Water in the Weddell Sea during 1992–2020 has also been revealed and is attributed to reduced sea ice production over the southern Weddell continental shelf related to the Interdecadal Pacific Oscillation and the variability in the Amundsen Sea Low. Though significant advances have been achieved, there is an urgent need to enhance and improve both observations and model performances for better understandings and projections of the formation, transformation, and transport of the water masses in the Southern Ocean.</p>