Background: Although flowers of Panax ginseng Meyer (FPG), Panax quinquefolius L. (FPQ), and Panax notoginseng Burk. (FPN) have been historically used as both medicine and food, each is used differently in practice. Methods: To investigate the connection between components and enhancing immunity activity of FPG, FPQ, and FPN, a method based on a rapid LC coupled with quadrupole time-of-flight MS and immunomodulatory activity study evaluated by a carbon clearance test were combined. Results: According to quantitative results, the ratio of the total content of protopanaxatiol-type ginsenosides to protopanaxadiol-type ginsenosides in FPN was 0, but ranged from 1.10 to 1.32 and from 0.23 to 0.35 in FPG and FPQ, respectively. The ratio of the total content of neutral ginsenosides to the corresponding malonyl-ginsenosides in FPN (5.52 ± 1.33%) was higher than FPG (3.2 ± 0.64%) and FPQ (2.39 ± 0.57%). The colorimetric analysis showed the content of total ginsenosides in FPQ, FPG, and FPN to be 13.75 ± 0.60%, 17.45 ± 0.42%, and 12.45 ± 1.77%, respectively. The carbon clearance assay indicated that the phagocytic activity of FPG and FPQ was higher than that of FPN. A clear discrimination among FPG, FPQ, and FPN was observed in the principal component analysis score plots. Seven compounds were confirmed to contribute strongly by loading plots, which may be the cause of differences in efficacy. Conclusion: This study provides basic information about the chemical and bioactive comparison of FPG, FPQ, and FPN, indicating that protopanaxtriol-type ginsenosides and malonyl-ginsenosides may play a key role in their enhancing immunity properties.