Xanthomonas citri pv. citri (Xcc), a gram-negative bacterium, is the causal agent of citrus canker, one of the most devastating diseases threatening the citrus industry worldwide. Understanding the diversity and population structure of Xcc is a prerequisite for disease epidemiological monitoring and effective disease management. Recent characterization of the clustered regularly interspaced short palindromic repeats (CRISPR)/cas (CRISPR-associated proteins genes) system with a highly variable repeat number among species provides a new molecular typing method for bacterial genetic analysis. In this study, we performed systematic in silico analyses of 28 Xcc genomes and identified a credible CRISPR/cas in Xcc strains. Further analysis of CRISPR polymorphisms (repeat number and spacer types) in 129 XccA strains collected from six provinces in China identified 15 types of CRISPR arrays with 25 spacers. Phylogenetic analysis of Xcc strains based on the CRISPR locus produced a more reliable and accurate typing result compared to the commonly used loci. In addition, seven associated cas genes—cas1, cas2, cas3, cas4, cas5, cas7 (csd2), and cas8 (csd1)—were found located adjacent to the CRISPR array. BLAST results showed > 99% similarity of seven cas genes among Xcc strains. Homology analysis of spacer sequences showed that six spacers had possible phage/prophage origin. The characterization of the CRISPR/cas system among Xcc strains provided an updated strain typing method for Xcc diversity analysis and yielded a panoramic view of CRISPR evolution for further studies of Xcc-phage interactions.