Paddy soil samples were collected from six provinces of China, and an anaerobic incubation test was conducted to examine the microbial Fe(III) reduction potential under the conditions of different flooding time and with glucose, pyruvate, lactate, or acetate as the sole carbon source. The results showed that flooding time had significant effects on the eigenvalue of Fe(III) reduction, Vmax, with the order of 20 d > 30 d > 12 d > 1 d > 5 d, which suggested that the difference in the microbial community structure in different flooding periods was the main reason inducing the different potential of Fe(III) reduction. In all test flooding periods, glucose and pyruvate were the superior carbon sources, with the Fe(III) reduction rate being 88.1%-99.9% and 58.0%-97.9%, respectively. When lactate was amended, the Fe(III) reduction rate varied greatly among different paddy soils. For the paddy soils from Hunan and Zhejiang, the Fe(III) reduction rate during flooding period could reach 87.1%-100%; while for other soils, it was 5.0%-49.4% in the first 5 days of flooding and 52.2%-99.9% in 12 days after flooding. When acetate was used as a carbon source, the Fe(III) reduction rate increased with flooding time. Especially in the paddy soil from Zhejiang, the Fe(III) reduction rate changed greatly from 5.3% to 75.8%.