In order to screen out the key genes involved in the response of rice to cyanide stress and cyanide metabolism in rice plants, the gene expression characteristics of leaves and roots of rice seedlings under the stress of potassium cyanide and potassium ferricyanide were analyzed by Agilent 4×44 K rice genome chip. The results showed that 1841 and 3037 differentially expressed genes in rice roots and 734 and 1805 differentially expressed genes in rice leaves were found under potassium cyanide and potassium ferricyanide treatments, respectively. Under potassium cyanide treatment, the up-regulated expression multiples of genes related to cell wall metabolism and stress resistance in roots. Under potassium ferricyanide treatment, the up-regulated expression were the detoxification-related genes in rice leaves. The results showed that cyanide could induce the differential expression of genes in rice. There were great differences in the expression of genes related to detoxification and stress resistance, cell wall and secondary metabolic pathways and transcription factors. These results revealed detoxify cyanide metabolism through metabolic processes such as active absorption and transport to reduce plant damage. The roots and leaves of rice may serve the main organism for responsing to cyanide stress by self-regulation.