Agricultural floods in the middle and lower reaches of the Yangtze River, known as the “land of fish and rice” in China, have increased both in areal coverage and frequency over the past 50 years, presenting a grave challenge to sustainable development and food security in the region. Studying the spatiotemporal variation characteristics of agricultural floods in this region is thus important for providing a scientific basis for regional flood control and disaster mitigation. We used variation trend analyses, Mann–Kendall tests, wavelet analyses, and center of gravity modeling to study spatiotemporal changes in agricultural floods in the study area, based on agricultural flood indicators. Changes in agricultural flood frequency showed an overall increasing trend. The frequency of floods changed abruptly in 1990, with the average frequency of floods per station increasing by 0.2086/year from 1991 through 2018, characterized by multiple time-scale changes. The time scale of 17 years had three low–high cycles, that of eight years had six, and that of four years had 13. Agricultural floods in the study area were concentrated in the southern Yangtze River and mainly occurred in northeastern Jiangxi Province and the southeastern Zhejiang Province. The area with high agricultural flood indices increased. Agricultural floods were closely related to the Yangtze River and the direction of the gravity center of agricultural floods was similar to that of the river. Affected by precipitation intensity and frequency, the gravity center fluctuated greatly and generally alternated from southwest to northeast.