Abstract Mutations in SF3B1 are common in many types of cancer, promoting cancer progression through aberrant RNA splicing. Recently, mRNA nuclear export has been reported to be defective in cells with the SF3B1 K700E mutation. However, the mechanism remains unclear. Our study reveals that the K700E mutation in SF3B1 attenuates its interaction with THOC5, an essential component of the mRNA nuclear export complex THO. Furthermore, the SF3B1 mutation caused reduced binding of THOC5 with some mRNA and inhibited the nuclear export of these mRNAs. Interestingly, overexpression of THOC5 restores the nuclear export of these mRNAs in cells with the SF3B1 K700E mutation. Importantly, other types of cancer-associated SF3B1 mutations also inhibited mRNA nuclear export similarly, suggesting that it is common for cancer-associated SF3B1 mutations to inhibit mRNA nuclear export. Our research highlights the critical role of the THOC5–SF3B1 interaction in the regulation of mRNA nuclear export and provides valuable insights into the impact of SF3B1 mutations on mRNA nuclear export.