Uncoordinate-45B (UNC-45B) is a myosin chaperone in striated muscles. Heat shock leads to myosin denaturation, and UNC-45B is involved in myosin refolding. Pacific bluefin tuna (PBT) was chosen for this study because of its high value and severe “burnt meat” problem in summer. cDNA cloning and expression analysis were carried out to evaluate the heat stress response of PBT UNC-45B. The cDNA of PBT unc-45b was cloned, and two isoforms were detected successfully. Isoform 1 consisted of 2994 bp encoding 931 amino acids, and isoform 2 consisted of 3071 bp encoding 930 amino acids. To clarify the effects of heat stress on UNC-45B, cultured PBT were sampled in summer (29.2 °C) and winter (20.9 °C), and analyzed by qPCR and immunoblotting. Compared with winter, both transcriptional and translational expression of UNC-45B in summer were dramatically higher. In addition, from the mRNA expression results, we found that PBT UNC-45B isoform 2 mainly responded to heat stress. Our findings indicate that an increase in UNC-45B expression levels can sensitively reflect the heat stress response in PBT. Therefore, UNC-45B may be considered as a candidate biomarker to evaluate heat stress tolerance in PBT. This will improve aquaculture development by enabling the selection of heat stress-tolerant juveniles.