Two undescribed letendrones A‐B (1‐2), along with three known compounds, ZL‐6 (3), dankasterone B (4) and minimoidione B (5) were isolated from the Aquilaria‐derived fungus Letendraea helminthicola A820. The structures of 1 and 2 were established by analysis of spectroscopes including 1D/2D NMR, IR, UV, and HRESIMS. Among them, the configuration of 1 was further confirmed by single‐crystal X‐ray diffraction. Letendrones A and B were the new phenalenyl derivatives with radical form that were firstly found in nature. In addition, bioactivity of these compounds was evaluated and compounds 3‐5 exhibited inhibitory activity against LPS‐induced NO production in macrophages with IC50 values of 4.64, 13.90, and 34.07 μM. Furthermore, potential targets of the new compounds were analyzed by molecular docking in silico. As a result, compound 1 showed high binding with predicted 5‐HT2c receptor (∆G=‐8.2 kcal/mol) potentially associated with depression disease, and compound 2 showed significant connection with phosphodiesterase 3A (∆G=‐9.4 kcal/mol) probably against cardiovascular disorders. Our findings firstly reported the high symmetry phenalenyl compounds from natural products which would provide a basis for further development and utilization of the secondary metabolites from the endophytic fungus Letendraea helminthicola A820.