Heme oxygenase-1/CO protects cancer cells from oxidative stress, but the gas-responsive signaling mechanisms remain unknown. Here we show using metabolomics that CO-sensitive methylation of PFKFB3, an enzyme producing fructose 2,6-bisphosphate (F-2,6-BP), serves as a switch to activate phosphofructokinase-1, a rate-limiting glycolytic enzyme. Stress-induced CO inhibits cystathionine beta-synthase (CBS), and thereby modulate methylation of many proteins including PFKFB3, an switching enzyme determining the balance of glucose metabolism between glycolysis and pentose phosphate pathway. In several different cancer cell lines derived from human, PFKFB3 is asymmetrically di-methylated at R131 and R134 through modification by protein arginine methyltransferase-1. HO-1 induction or CO results in reduced methylation of PFKFB3 in varied cancer cells to suppress F-2,6-BP, shifting glucose utilization from glycolysis toward pentose phosphate pathway. Loss of PFKFB3 methylation depends on the inhibitory effects of CO on heme-containing cystathionine beta-synthase (CBS). CBS modulates remethylation metabolism, and increases NADPH to supply reduced glutathione, protecting cells from oxidative stress and anti-cancer reagents. Once the methylation of PFKFB3 is reduced, the protein undergoes polyubiquitination and is degraded in proteasomes. CBS knockdown in HCT116 cells stimulates cancer cell proliferation, so far as seen in a hepatic metastatic model of the cancer xenografts. Under the given condition, tumors increased GSH levels but with decreasing glutathione S-sulfonate, a product derived from GSS − in vivo. These results suggest that the CO/CBS determines the balance between NADPH and endogenous persulfides, and CBS-sensitive PFKFB3 methylation 1 determines directional glucose utilization to ensure resistance against oxidative stress for cancer cell survival.