This paper employed UPLC-Electrospray Ionization /Quadrupole-Time of Flight-Mass /Mass Spectrometry( UPLC-ESI/Q-TOF-MS/MS) to analyze the chemical constituents in the stems of Nelumbo nucifera. The stems of N. nucifera were extracted with 75% methanol, and we applied an Agilent Zorbax SB-Aq column (2.1 mm x 100 mm, 1.8 μm) to UPLC analysis with water methanol-water( containing 0.05% formic acid) in gradient as mobile phase. The eluates were then detected by ESI-Q-TOF-MS/MS. Results indicated that 22 benzylisoquinoline alkaloids were indendified. Among them, one alkaloid may be a new compound and a component was found in the Lotus for the first time. We fully identify the composition of the Lotus stems for the first time, Which could provides theoretical foundation for further study and utilization of the medicinal resources.