Alternative splicing is crucial for post-transcriptional regulation and is responsible for transcriptome and proteome diversity. In recent years, with the completion of transcriptome sequencing of plants such as Arabidopsis thaliana, Oryzasativa, and Maize, researchers found that pre-mRNA alternative splicing in plant is involved with tissue differentiation and development, etc. In this work, RNA-seq data was downloaded from GEO database. Trimmomatic, Salmon, DESeq2, SUPPA2 and other tools were employed to detect expression genes and alternative splicing events in seed, root, leaf, flower, pedicel, internode and pod across the Arabidopsis. Then, differentially expressed genes and differential alternative splicing events were identified throughout 7 tissues. Furthermore, the comparison between leaves and flowers was taken as an example to display the corresponding biological functions. In this study, the tissue specificity of gene expression and alternative splicingin Arabidopsis was systematically investigated. It’s helpful for elucidating gene expression mechanism in plant genome.