The bacteria pathogenXanthomonas oryzaepv.oryzae(Xoo) infects rice and causes the severe disease of rice bacteria blight. As the central regulator of the salic acid (SA) signaling pathway, NPR1 is responsible for sensing SA and inducing the expression of pathogen-related (PR) genes in plants. Overexpression ofOsNPR1significantly increases rice resistance toXoo. Although some downstream rice genes were found to be regulated byOsNPR1, howOsNPR1affects the interaction of rice-Xooand altersXoogene expression remains unknown. In this study, we challenged the wild-type andOsNPR1-OErice materials withXooand performed dual RNA-seq analyses for the rice andXoogenomes simultaneously. InXoo-infectedOsNPR1-OEplants, rice genes involved in cell wall biosynthesis and SA signaling pathways, as well as PR genes and nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, were significantly upregulated compared to rice variety TP309. On the other hand,Xoogenes involved in energy metabolism, oxidative phosphorylation, biosynthesis of primary and secondary metabolism, and transportation were repressed. Many virulence genes ofXoo, including genes encoding components of type III and other secretion systems, were downregulated byOsNPR1overexpression. Our results suggest thatOsNPR1enhances rice resistance toXooby bidirectionally regulating gene expression in rice andXoo.