Abstract: Province-wide data on flood-destroyed and flood-affected crop areas across China covering a period of 1960–2013 were analyzed in this study for investigating their relations with climate indices, such as ENSO, NAO, IOD, PDO and AMO. Results indicated that: (1) agricultural flooding in northeast and south China tended to enhance under the influence of warm PDO and warm IOD events of the previous years. However, agricultural flooding in southwest China tended to decrease as a result of warm ENSO events of the previous years. Agricultural floods in coastal regions of southeast China were influenced by more than one climate index; (2) Agricultural floods of different time scales were subject to different degrees of correlations with climate indices. Remarkably, climate indices that were significantly correlated with agricultural floods were usually temporally enhancing. Relations between ENSO and agricultural floods across China were statistically strong with good persistency. Thus, ENSO can be taken as a suitable predictor for flood-affected and flood-destroyed crop areas across China. However, AMO cannot be taken as the predictor for flood-affected and flood-destroyed crop areas in China; (3) The combined influence of climate indices on flood-affected and flood-destroyed crop areas across China did not have a firm spatiotemporal pattern. However, specific groups of climate indices can have definitive impacts on flood-affected and flood-destroyed crop areas over specific regions. Findings of this study can help predict flood-affected and flood-destroyed crop areas across provinces of China, and hence plan and manage agricultural activities in China.