Abstract An application of mass spectrometric methods has been developed to characterize, prepare and quantitatively analyze three bisbenzylisoquinoline alkaloids (liensinine, isoliensinine and neferine) from embryo of the seed of Nelumbo nucifera GAERTN. Initially, an analytical method based on liquid chromatography electrospray ionization tandem mass spectrometry (LC–ESI-MS/MS) with positive ionization mode using a MonoChrom C18 column (4.6 mm × 250 mm i.d. 10 μm) has been developed to characterize liensinine, isoliensinine and neferine, and then scaled up to purify them on a 21.4 mm × 250 mm preparative column. The structures of liensinine, isoliensinine and neferine were elucidated by NMR. Finally, a LC–MS/MS determination method, successfully applied to separation within 3 min, was developed for high throughput simultaneous measurment of liensinine, isoliensinine, and neferine in the extract samples. Multiple reaction monitoring (MRM) was used to monitor the transition of the protonated molecules m/ z 611, 611, 625 [ M + H] + to the product ions m/ z 206, 192, 206 for analysis of liensinine, isoliensinine and neferine. The LC–MS/MS system was linear in the concentration range of 0.0247–6.02 μg/ml with correlation coefficients of r 2 > 0.992. The quantitative method was validated, with an S/N = 3 detection limit of 0.15 ng for liensinine, 0.19 ng for isoliensinine and 0.12 ng for neferine. The mass fractions of liensinine, isoliensinine, and neferine in the crude extract and the phenolic alkaloid sample of embryo of the seed of N. nucifera GAERTN. were 16.5 ± 1.1 and 228.6 ± 11.9 for liensinine (mg/g), 45.7 ± 1.8 and 640.7 ± 15.2 for isoliensinine (mg/g), 59.7 ± 6.4 and 58.8 ± 9.8 for neferine (mg/g).