The cultivated land-use transition (CLUT) is the morphological result of changes in the cultivated land-use mode over time, and the result of the interaction and mutual restriction of the human land system. This paper applies a “spatial–functional” integrated framework to understand the structure and functioning of CLUTs, and quantitatively evaluates and visualizes CLUTs in the major grain-producing area in southern China. The results show that (1) the comprehensive CLUT index in the middle and lower reaches of the Yangtze River changed from 0.0480 to 0.0711 from 2001 to 2019 and indicated significant differences in the transition index between different regions. (2) The CLUT identified a positive aggregation effect under a 5% significance during the period, and the agglomeration degree of the spatial and functional transitions strengthened, which increased from 0.3776 to 0.4673 and from 0.2127 to 0.2952, respectively. (3) The gravity center of the CLUT demonstrated a pattern of migration from the southwest to the northeast, and the migration speed of the gravity center decreased from 2.9401 km/year to 1.2370 km/year. The migration direction of the gravity center for the spatial transition is opposite to the functional transition, and the migration speed of the gravity center for the spatial and functional transitions decreased from 8.3573 km/year to 1.0814 km/year, and from 3.2398 km/year to 1.0254 km/year, respectively. To address this transition, policymakers should formulate differentiated policies to promote the sustainable use of cultivated land through the spatial and functional transition of major grain-producing areas.