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Alternative splicing (AS) is an important mechanism by which eukaryotes regulate transcription and protein diversity. The dynamic changes in AS that occur on a genome-wide scale during interactions between plant roots and pathogens remain unknown. Here, we used the interaction between Arabidopsis and Ralstonia solanacearum as a model to explore the AS changes that take place during the response of roots to infection by means of high-throughput RNA-sequencing. We showed that dynamic changes in AS occur much earlier than changes at the level of transcription during R.solanacearum infection. Comparing genes that are regulated at the transcriptional and AS levels indicated that there are few common genes between differentially spliced genes (DSGs) and differentially expressed genes (DEGs). The functional gene ontology (GO) analysis identified that the enriched GO terms for the DSGs were different from those of the DEGs. The DSGs were over-represented in GO terms associated with post-transcriptional and translational regulations, suggesting that AS may act on RNA stability and during post-translation, thus affecting the output of plant defense molecules. Meanwhile, changes in DSGs were infection stage-specific. Furthermore, the nucleotide binding domain and leucine-rich repeat proteins and receptor-like kinases, key regulators in plant immunity, were shown to undergo dynamic changes in AS in response to R. solanacearum. Taken together, AS, along with transcription, modulates plant root defense to R. solanacearum through transcriptome reprogramming.