Whether China can achieve the United Nations’ Sustainable Development Goals (SDGs) largely depends on the ability of main food-producing areas to cope with multiple land use change challenges. Despite the fact that the Yangtze River basin is one of the key regions for China’s food security, the spatiotemporal dynamics of cropland abandonment and recultivation remain largely unexplored in this region. The present study assesses the evolution of the agricultural system within the Yangtze River basin between 2000 and 2020 by mapping cropland abandonment and recultivation using MODIS time series and multiple land cover products. The results highlight a widespread cropland abandonment process (i.e., 10.5% of the total study area between 2000 and 2020), predominantly in Western Sichuan, Eastern Yunnan, and Central Jiangxi. Although 70% of abandoned cropland is situated in areas with slopes less than 5°, the highest rates of abandonment are in mountainous regions. However, by 2020, 74% of this abandoned cropland had been recultivated at least once, whereas half of the abandoned croplands got recultivated within three years of their initial abandonment. Hence, as this is one of the first studies that unravels the complex interaction between cropland abandonment and recultivation in a spatiotemporal explicit context, it offers (i) scientists a novel methodological framework to assess agricultural land use issues across large geographical entities, and (ii) policy-makers new insights to support the sustainable transition of the agricultural sector.