The current knowledge of the transcriptome is limited to understand the exact molecular mechanism of the ion-implantation biological effects on cereals. In order to investigating the overall characteristics of the transcript profiles associated with these puzzling biological effects. We used the Agilent Rice Oligo Microarray （4×44K）Genome Array to learn the molecular mechanism in rice responding to ion-implantation. Rice seeds were implanted by the Nitrogen ion beam and their vigor index was investigated at ten days after germination. Total RNAs was extracted from the rice seedlings at 96 hour after germination and hybridized by the genome genechip. The results of measuring of the vigor index showed that lower-dose implantation of the nitrogen ion beam (6×1017 N+/cm2) promoted the vigor index of the rice seedlings and the higher-dose implantation (9×1017 N+/cm2) damaged the rice seedlings because of the smaller vigor index than the control. The analysis of the genechip array showed that there were 982 transcripts expressed differentially (fold change＞2 and P value＜0.05) including 429 up-regulated transcripts and 553 down-regulated transcripts under the dose3 6×1017 N+/cm2. 30 out of the 553 down-regulated transcripts were involved in 48 pathways. 14 out of these 30 transcripts were associated with more than two interrelated pathways. Os04g0518400 (Phenylalanine ammonia-lyase 2 (PAL; EC 184.108.40.206; down-regulated 3.3 folds; p value=0.005) were involved in 7 pathways, Os07g0446800 (Hexokinase; dwon-regulated 2.8 folds; p value =0.006) were involved in 12 pathways, and Os02g0730000 (Mitochondrial aldehyde dehydrogenase ALDH2a; down-regulated 2.2 folds; p value=0.019) were involved in 13 pathways. These results revealed that down-regulated genes involving important pathways were compatible with the distinct cellular events in response to implantation of low-energy ion beam and supplied the first comprehensive and comparative molecular information for further understanding the mechanism underlying implantation of the low-energy nitrogen ion beam.