In this study, miraculin–like protein 2(MLP2–1) gene of kumquat was cloned and transformed into wild–type Arabidopsis (Col–1) by Agrobacterium–mediated infiltration. The transcriptional data of transgenic Arabidopsis under colds tress was analyzed, which revealed the mechanism of MLP2–1 gene in Arabidopsis. The results showed that transgenic Arabidopsis had higher resistance than wild–type Arabidopsis under cold stress; comparing with the wild–type Arabidopsis, transcriptome analysis showed that 551 genes were up–regulated and 871 genes were down–regulated in total 1 422 differently expressed genes. Among of them, 474 annotations was from KEGG, 1 208 from GO and 603 from COG after functional annotation. KEGG analysis showed that differentially expressed genes mainly involved in the plant hormones signal transduction pathway, which will provided a foundation for further studying MLP2–1 functions of kumquat．