In recent years, there has been a notable increase in the frequency and intensity of floods and heavy rains, which has resulted in the frequent inundation of rice-growing areas. Flooding during the heading–flowering stages of early rice can result in significant yield losses. To elucidate the response of rice to sediment content, flooding, and drainage processes and their underlying mechanisms, a pot experiment was conducted to investigate the effects of sediment contents (S₁: 0, S₂: 0.10 kg m⁻³, and S₃: 0.25 kg m⁻³), flooding time (F₁: 3 days and F₂: 6 days), and drainage time (D₁: 3 days and D₂: 6 days) during the heading–flowering stage on the oxidation resistance and grain yield of early rice in the Poyang Lake Region. At the same time, an experimental control group (CK) was set up with no sediment, no flooding, or no drainage treatment. The results showed that the flag leaf area of S₁F₁D₂ treatment was diminished by flooding. The relative chlorophyll content (SPAD) reached its lowest value prior to drainage. The treatment of S₂F₂D₁ showed the greatest decrease in SPAD value of 41.57%, which was only 53.88% of that of the control treatment. The activity of superoxide dismutase (SOD), peroxidase (POD), and the content of malondialdehyde (MDA) were observed to increase during the flooding period in comparison to the control treatment. The maximum values for these parameters were recorded at 5.68, 3.09, and 1.9 times higher than those of the control treatment, respectively. However, a decrease was observed after drainage. Furthermore, the occurrence of flooding during the early rice heading–flowering stage resulted in a notable reduction in the grain number per spike and the fruiting rate, consequently leading to a considerable decline in grain yields, with a decrease ranging from 31.81% to 69.96%. The findings indicate that flooding during the heading–flowering stage resulted in a reduction in early rice grain yield yet enhanced the antioxidant capacity of the leaves. Regression analyses indicated that a prediction model for the actual yield after flooding stress at the heading–flowering stage of early rice could be constructed using SFW as the independent variable. The findings of this study provide a theoretical basis for the formulation of a scientific and reasonable drainage scheme with the objective of reducing yield loss following rice flooding in the southern rice-growing region of China.