Abstract: 【Objective】This study aimed to analyze genetic variations and fruit metabolic changes in Zanthoxylum armatum under spaceflight conditions， to provide references for screening and identifying space-mutagenized Zanthoxylum armatum populations， germplasm innovation and new cultivar breeding of prickly ash.【Method】Two Zanthoxylum armatum cultivars， Zaoshujiuyeqing （ZSJ） and Tengjiao （TJ） were used as research subjects， and the non-mutagenized samples as control （CK）. Based on reference genomes of Zanthoxylum armatum， genome resequencing， and untargeted metabolomic analysis were utilized to perform genomic mutation detection and analysis of pre-spaceflight samples before （ZSJ-CK and TJ-CK） and post-spaceflight samples （ZSJ-HT and TJ-HT）. The GO functional annotation and KEGG signaling pathway analysis were performed on mutant genes， and KEGG metabolic pathway enrichment analysis were performed on differential metabolites in pre-spaceflight and post-spaceflight samples.【Result】The single nucleotide variant （SNV） number of ZSJ-HT samples was 1.76 times that of ZSJ-CK samples； the insertion/deletion variants （InDel） number of ZSJ-HT samples was 2.12 times that of ZSJ-CK samples. For mutation number of InDel at each mutant fragment length， the InDel number of ZSJ-HT samples was higher than that of ZSJ-CK samples， while the InDel number of TJ-HT samples was higher than that of TJ-CK samples. In the groups of ZSJ-HT vs ZSJ-CK and TJ-HT vs TJ-CK， the total numbers of SNVs were 65150 and 68473， the total numbers of InDels were 1615 and 2430， and the numbers of protein-coding genes with meaningful mutations were 936 and 1034， respectively. GO functional terms with the highest number of annotated mutated genes in the groups of ZSJ-HT vs ZSJ-CK and TJ-HT vs TJ-CK included metabolic processes， organic substance metabolic processes， integral component of membrane， and zinc ion binding. The KEGG signaling pathways with the largest number of mutant genes were metabolic pathways， biosynthesis of secondary metabolites， plant-pathogen interaction， and plant hormone signal transduction. In the ZSJ-HT vs ZSJ-CK group， the contents of 264 metabolites significantly increased， while the contents of 325 metabolites significantly decreased. In the TJ-HT vs TJ-CK group， the contents of 398 metabolites significantly increased， and the contents of 271 metabolites significantly decreased. KEGG metabolic pathway enrichment analysis revealed that the most enriched pathways in the ZSJ-HT vs ZSJ-CK group were flavonoid and flavonol biosynthesis and flavonoid biosynthesis， whereas the most enriched pathways in the TJ-HT vs TJ-CK group were ABC transporters and phenylpropanoid biosynthesis.【Conclusion】Spaceflight conditions induce considerable changes in all protein-coding genes in genomes and metabolite contents and compositions of mature fruits， and the screened metabolic pathways with significant enrichment and significant differential metabolites can be used in further screening and identification of mutagenized Zanthoxylum armatum populations.