The dried flower buds of Magnolia biondii Pamp (herbal name, Xin-Yi) are a traditional Chinese medicine with a long history of clinical use in the treatment of allergic rhinitis and sinusitis. However, the constituents responsible for its antiallergic effects remain unidentified. In the present study, a novel bisepoxylignan, isoeudesmin (1), and eight known bisepoxylignans, pluviatilol (2), eudesmin (3), magnolin (4), lirioresinol-B dimethyl ether (5), epimagnolin B (6), kobusin (7), aschantin (8), fargesin (9), were isolated from effective fractions through antiallergic bioassay-guided procedures using mouse bone marrow-derived mast cells (BMMCs) and IgE-induced passive cutaneous anaphylaxis mice. The compound structures were elucidated through nuclear magnetic resonance and mass spectrometry analyses. Compound 1 and compounds 2–6 and 9 exhibited antiallergic effects without affecting the viability of BMMCs. Compounds 2 and 9 showed the strongest effects with IC50 values of 52.18 and 93.03 μM, respectively. In this paper, the structure–activity relationship between these bisepoxylignans and their antiallergic effects is discussed. After evaluating the intensity of the antiallergic effects of the extracts, further separating the fractions, and isolating the purified compounds, we concluded that biosepoxylignans are the main constituents in Xin-Yi contributing to its anti-allergic efficacy.