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Cotton (Gossypium spp.) is an important industrial crop, but it is vulnerable to waterlogging stress. The relationship between cotton yields and waterlogging indicators (CY-WI) is fundamental for waterlogging disaster reduction. This review systematically summarized and analyzed literature containing CY-WI relations across 1970s–2020s. China conducted the most CY-WI experiments (67%), followed by Australia (17%). Recent decades (2010s, 2000s) contributed the highest proportion of CY-WI works (49%, 15%). Surface waterlogging form is mostly employed (74%) much more than sub-surface waterlogging. The flowering and boll-forming stage, followed by the budding stage, performed the most CY-WI experiments (55%), and they showed stronger negative relations of CY-WI than other stages. Some compound stresses enhance negative relations of CY-WI, such as accompanying high temperatures, low temperatures, and shade conditions, whereas some others weaken the negative CY-WI relations, such as prior/post drought and waterlogging. Anti-waterlogging applications significantly weaken negative CY-WI relations. Regional-scale CY-WI research is increasing now, and they verified the influence of compound stresses. In future CI-WI works, we should emphasize the influence of compound stresses, establish regional CY-WI relations regarding cotton growth features, examine more updated cotton cultivars, focus on initial and late cotton stages, and explore the consequence of high-deep submergence.