Sirtuin-3 (Sirt3), a sub-family member of the nicotinamide adenine dinucleotide-dependent histone deacetylases, has been reported to be involved in mitochondrial oxidative stress regulation, mitochondrial calcium management, mitophagy activation, and mitochondrial energy metabolism. The aim of our study was to explore the functional role of Sirt3 in colorectal cancer stress, focusing particularly on its effects on mitochondrial fission. Our study demonstrated that Sirt3 was highly upregulated in colorectal cancer cells compared to normal rectal mucosa cells. However, the genetic ablation of Sirt3 reduced colorectal cancer cell viability, mobility and proliferation. At the molecular level, we found that Sirt3 knockdown suppressed the expression of adhesive factors and cyclins. Furthermore, Sirt3 deletion was also associated with mitochondrial membrane potential reduction, ROS overproduction, mPTP opening, mitochondrial pro-apoptotic upregulation, and caspase-9-related death programme activation. Furthermore, we determined that Sirt3 regulated the colorectal cancer stress response by modulating mitochondrial fission. The loss of Sirt3 triggered fatal mitochondrial fission by suppressing the Akt/PTEN pathway. Re-activation of the Akt/PTEN pathway combatted mitochondrial fission and promoted colorectal cancer mobility, survival, and growth. Altogether, these findings provide an additional rationale for the function of Sirt3 in supporting the growth and survival of colorectal cancer.