Understanding the process of crop evapotranspiration (ETc) and developing models for estimating ETc are crucial to efficiently schedule irrigation and enhance efficient water use. Here, we investigated variations of ETc and local crop coefficient (Kc = ETc / ETo, where ETo is the reference evapotranspiration) in a rotated flooded rice-winter wheat system using ETc data based on the Bowen-ratio energy balance method from 2016 to 2020. We propose a modified Kc model for estimating daily ETc, which includes a density coefficient (a function of fraction of canopy cover) and incorporates the effect of plant temperature constraint, leaf senescence, and water stress on ETc. Results indicated that the total ETc over whole growth stage for flooded rice and winter wheat field was 500.2 ± 62.5 and 298.6 ± 28.3 mm (means ± standard deviation), respectively. The values of local Kc at the initial, middle, and late stages were 0.83 ± 0.14, 1.11 ± 0.06, and 0.99 ± 0.15, respectively, for flooded rice and 0.71 ± 0.08, 0.86 ± 0.06, and 0.76 ± 0.08, respectively, for winter wheat. There was no water stress over the entire season of the flooded rice-winter wheat rotation system except for some days with water draining in paddy rice field. Heat stress in summer adversely affected the ETc of rice. The modified Kc model can well reproduce the values of daily ETc for both flooded rice and winter wheat, and improved the accuracy by 6~9% compared to the FAO 56 Kc model using tabulated values after adjustment. The regression coefficient, coefficient of determination, root mean squared error and modeling efficiency between measured ETc and estimated by the modified Kc model were 0.99, 0.89, 0.55 mm d−1 and 0.89, respectively, for flooded rice, and 1.03, 0.85, 0.55 mm d−1 and 0.82, respectively, for winter wheat. Therefore, the modified Kc model could reasonably predict ETc for flooded rice and winter wheat and can serve as a useful tool to improve water use.