Cyberlindnera fabianii is a Baijiu-associated non-Saccharomyces yeast that may encounter transient heat stress during fermentation, but the mechanisms underlying its thermotolerance remain poorly understood. Here, we evaluated heat survival, culture turbidity, culturability, JC-1-based relative mitochondrial polarization, and transcriptomic responses of C. fabianii at 45 °C under different glucose concentrations. C. fabianii showed higher CFU-based survival than Saccharomyces cerevisiae after 2 h of heat exposure. During prolonged incubation, 30% glucose improved culturability and was accompanied by higher relative mitochondrial membrane potential (MMP), less disrupted JC-1 staining patterns, weaker repression of glycolysis- and TCA-cycle-related transcripts, and increased PPP-related transcript levels together with upregulation of ROS-scavenging genes. These findings indicate a glucose-associated improvement in heat-stress tolerance, particularly involving early maintenance of mitochondrial polarization and metabolic/redox-related transcriptional responses; however, the current data do not determine whether this effect is transient or long-lasting. Under glucose-limited conditions, glycerol or xylose co-feeding increased turbidity and partially supported CFU retention, with substrate-dependent differences in extracellular glucose consumption. Overall, these findings suggest that glucose availability is closely associated with thermotolerance and mitochondrial polarization in C. fabianii, and that, in liquid culture, selected co-substrates may partially reproduce aspects of the high-glucose-associated phenotype without requiring comparable glucose supplementation.