Objective To compare the differences in alkaloids between Nelumbinis Semen and Nelumbinis Plumula and their inhibitory effects on the proliferation of HepG2 cells, and investigate the material basis for their anti-cancer activity differences. Methods Simultaneous Thermal Analysis was used to preliminarily compare the component differences between Nelumbinis Semen and Nelumbinis Plumula. Alkaloids were extracted from them by both using reflux extraction, and their contents were measured by UV and HPLC methods. The CCK-8 method was used to assess the in vitro inhibitory effects of the alkaloids on the HepG2 cells, and to verify pharmacological differences. Results Simultaneous thermal analysis revealed distinct peak shapes, positions, and sizes in the thermal analysis curves of Nelumbinis Semen and Nelumbinis Plumula at respective temperature stages. The contents of total alkaloids showed as follows: the total alkaloids in Nelumbinis Plumula > total extract of Nelumbinis Plumula > the total alkaloids in Nelumbinis Semen. The total alkaloids in Nelumbinis Plumula effectively inhibited HepG2 cell proliferation, while the total alkaloids in Nelumbinis Semen showed no impact. Conclusion Differences in the composition and content of alkaloids may be key factors underlying the biological activities differences between Nelumbinis Semen and Nelumbinis Plumula. This study provided a basis for exploring the material foundation of the differential efficacy and properties of Nelumbinis Semen and Nelumbinis Plumula, which could support their rational clinical application.