<span class="paragraphSection"><div class="boxTitle">Abstract</div><span style="font-style: italic;">Mycobacterium tuberculosis</span> (<span style="font-style: italic;">Mtb</span>) possesses a type III-A CRISPR-Cas system and has anti-plasmid immune activity. However, whether this system exerts other additional functions remains to be characterized. Here, we investigated the <span style="font-style: italic;">in vivo</span> roles of the <span style="font-style: italic;">Mtb</span> CRISPR-Cas system. We show that this system is transcriptionally dependent and exhibits limited ability to counteract exogenous nucleic acids, primarily through the Csm6 protein rather than the Cas10 HD domain. We further demonstrate that this system plays a role in mitigating oxidative stress and antibiotic treatment, a function mainly mediated by the Cas10 HD domain. Importantly, through transposon library screening, we identified oligoribonuclease (Orn) as a regulatory protein of the <span style="font-style: italic;">Mtb</span> CRISPR-Cas system. Deletion of the <span style="font-style: italic;">orn</span> gene resulted in elevated c-di-GMP levels. A subsequent biotin-labeled c-di-GMP pull-down assay identified the transcriptional regulator Rv3058. Knockdown of <span style="font-style: italic;">rv3058</span> significantly increased <span style="font-style: italic;">cas6</span> promoter activity, and its transcriptional repressor function was directly modulated by c-di-GMP. This regulatory pathway enhances stress defense by activating multiple protective pathways, including DNA repair, cell envelope maintenance, and iron homeostasis regulation. Together, we conclude that the regulation of the CRISPR-Cas system by Orn-mediated c-di-GMP contributes to oxidative and antibiotic stress responses