Lily bulbs (Lilium lancifoliumThunb.) are rich in phytochemicals and have many potential biological activities which could be deep-processed for food or medicine purposes. This study investigated the effects of microwaves combined with hot-air drying on phytochemical profiles and antioxidant activities in lily bulbs. The results showed that six characteristic phytochemicals were identified in lily bulbs. They also showed that with an increase in microwave power and treatment time, regaloside A, regaloside B, regaloside E, and chlorogenic acid increased dramatically in lily bulbs. The 900 W (2 min) and the 500 W (5 min) groups could significantly suppress the browning of lily bulbs, with total color difference values of 28.97 ± 4.05 and 28.58 ± 3.31, respectively, and increase the content of detected phytochemicals. The highest oxygen radical absorbance activity was found in the 500 W, 5 min group, a 1.6-fold increase as compared with the control (57.16 ± 1.07 μmol TE/g DW), which was significantly relevant to the group’s phytochemical composition. Microwaves enhanced the phytochemicals and antioxidant capacity of lily bulbs, which could be an efficient and environmentally friendly strategy for improving the nutrition quality of lily bulbs during dehydration processing.