Purpose: Evaluate the value of bilateral final/baseline threshold level changes of lower cranial nerve MEPs in postoperative swallowing function deterioration prediction. Methods: Bilateral lower cranial nerve motor-evoked potentials (MEPs) were recorded in 51 patients who underwent treatment for skull base and brainstem tumors. Corkscrew-like electrodes were positione 2 cm below C3/C4 and Cz. The MEPs were recorded from different muscle groups, including the posterior pharyngeal wall muscle, tongue muscle, genioglossus muscle, and cricothyroid muscle through paired needle electrodes. Swallowing function was assessed clinically using the Mann Assessment of Swallowing Ability score before and after the procedure at 7 days, 1 month, and 3 months. Results: Bilateral final/baseline threshold level increases in lower cranial nerve MEPs under the dual monitoring were significantly correlated with postoperative swallowing function deterioration (r ¼ 0.660 at 7 days, r ¼ 0.735 at 1 month, and r ¼ 0.717 at 3 months; p , 0.05). Bilateral final/baseline threshold level changes of more than 20% were recorded in 23 of the 51 patients, with 21 patients experiencing swallowing function deterioration postoperatively. The other 28 patients had bilateral threshold level changes of less than 20%, with 26 patients maintaining or improving their swallowing function, and 12 of those patients presented transient deterioration of swallowing function in the early postoperative period. Conclusions: Dual monitoring of lower cranial nerves and their different muscle groups MEPs was a safe and effective way to predict postoperative swallowing function. An increase in bilateral final/baseline threshold level change of more than 20% was predictive of permanent swallowing deterioration, especially in patients with poor swallowing function preoperatively.