Mitochondrial components are of great importance for the maintenance of lens transparency. In our previous work, we confirmed that carbon monoxide (CO) can protect human and rabbit lens epithelial cells (LECs) from hydrogen peroxide (H2O2)-mediated apoptosis, while the mechanism remains undefined. Because CO can bind to mitochondrial cytochrome c oxidase (COX), we evaluated the effect of CO on the regulation of mitochondrial biogenesis and function in H2O2-treated rabbit LECs. To evaluate mitochondrial biogenesis, several mitochondrial transcription factors (PGC-1 alpha, NRF-1, and mtTFA) were detected by western blot analysis. To assess cellular metabolism, adenosine triphosphate (ATP) levels and COX enzymatic activity were measured. In addition, mitochondrial permeability transition pores (mPTP) opening, dissipation of mitochondrial membrane potential (Delta Psi m), cytochrome c mitochondrial translocation, and apoptotic molecules were also detected to evaluate mitochondrial apoptosis pathway. Furthermore, the interaction of Bcl-2 and COX was assessed by co-immunoprecipitation. Finally, CO-mediated regulation of cellular function was detected in Bcl-2-knockdown cells. Our results confirmed that CO pretreatment restored H2O2-induced down-regulation of mitochondrial transcription factors expression, COX activity and ATP production. Moreover, CO pretreatment attenuated mPTP opening, Aim loss, cytochrome c mitochondrial translocation, and activation of apoptotic molecules. Bcl-2 was identified to bind to COX, and silence of Bcl-2 expression prevented CO-regulated cellular metabolism and cytoprotection. These data suggest that CO modulates H2O2-induced cellular dysfunction by increasing mitochondrial biogenesis, enhancing cellular metabolism, and attenuating mitochondrial apoptosis cascade. Moreover, Bcl-2 expression was vital for CO to regulate cellular metabolism and cytoprotection in LECs.