We analyzed the spatio-temporal dynamics of land use and ecological carrying capacity in Huainan city with an improved ecological footprint model based on remote sensing and a social-economical system development index. The results showed that: from 1987 to 2012, the ecological carrying capacity per capita educed gradually in the beginning and then increased slowly with 2009 being the inflection point, which reflected the positive effects of new economic development mode and science technology; The ecological carrying capacity in Huainan exhibited strong spatio-temporal variability with an overal spatial pattern of high capacity in Southeast and North and low in West and an increasing fragmentation trend at the regional scale. The loss of farmland to mining sites and the formation of seeper collapse area were the main causes of capacity decline and spatio-temporal variability. The main types of land use transfer were farmland and building land, and water area increasingly exerted great influences on land use pattern. Our study suggests that one of the most effective ways for improving ecological carrying capacity in Huainan is to conduct comprehensive treatment in the collapse areas, such as changing seeper collapse area into farmland and building land.