Lilium dauricum is a rare and endangered species belonging to the family Liliaceae. The species contains several bioactive compounds used as functional foods and medicinal agents in Northeast Asia. This study aimed (1) to establish an in vitro bulblet culture using an air-lift bioreactor and callus culture for the conservation of L. dauricum and obtaining its bioactive compounds; (2) investigate the plant phenolic compounds from both cultures system. The highest bulblet production with 12.5-fold increase in growth rate was obtained using MS medium supplemented with 0.5 g L-1 BA and 3% sucrose. Addition of 7% sucrose facilitated bulblet enlargement, with approximate 2.5- and 7-fold increases in diameter and fresh weight, respectively. The highest rate of callus (100%) was obtained using a combination of 1.0 mg L-1 picloram and 0.5 mg L-1 Kinetin. The callus proliferation occurred on MS medium supplemented with 1.0 mg L-1 picloram, 0.25 mg L-1 kinetin, and 0.25 g L-1 casein hydrolysate. There was a significant difference in the total phenolic compound content of callus, which was 1.5-fold higher than that in the bulblets. These findings indicate a suitable system for optimizing both bulblet and callus culture of L. dauricum, therefore, providing useful bio-materials for industrial purposes and contributing to the conservation of this species.