As a new mutagen， lithium （⁷Li） ion beam plays an increasingly important role in crop mutation breeding. In this study， the characteristics of wheat DNA damage induced by ⁷Li ion beam irradiation treatment were explored by comet assay， and the transcriptional re-programming was preliminarily analyzed by transcriptome analysis. The wheat seedlings showed lower growth inhibition of wheat seedlings caused by ⁷Li ion beam irradiation， but seedlings leaf vein chlorosis to cracking， if compared with those treated by the conventional mutagenic gamma ray （γ）. Based on GO and KEGG functional analysis of differentially expressed genes （DEGs） induced by irradiation， DEGs induced by ⁷Li ion beam irradiation were mainly enriched in cell wall synthesis and metabolism and glycerolipid metabolic pathways， while DEGs induced by γ ray irradiation were mainly enriched in photosynthetic metabolic pathways. That suggested that cell wall synthesis and metabolism and glycerolipid metabolic pathways are likely modulated by ⁷Li ion beam irradiation， while photosynthetic metabolic pathways are likely modified by γ ray irradiation. Gained from the results of transcription factor analysis of two radiation-induced DEGs， several transcription factor families， such as MYB， WRKY， bHLH and NAC， might specifically respond to ⁷Li ion beam irradiation. The results of this study implied that ⁷Li ion beam irradiation specifically modify the transcriptional re-programming of Whirly family transcription factors to regulate DNA damage repair， while the conventional γ ray irradiation likely induced the E2F / DP family transcription factors to regulate DNA damage repair.