Two undescribed eudesmane‐type sesquiterpenoids together with four known compounds were isolated from Clonostachys sp. Y6‐1 associated. Their chemical structures were unambiguously determined by NMR, mass spectrometry, and 13C NMR calculation as well as DP4+ probability analyses. The absolute configurations of compounds 1 and 2 were determined by ECD calculation and X‐ray single‐crystal diffraction methods. Furthermore, all isolates were evaluated for in vitrocytotoxic activities against MCF‐7, HCT‐116, MDA‐MB‐231, and SW620 cancer cells. Among them, bioactivity evaluation of compound 5 revealed that weak activity (IC50 = 66.55 ± 0.82 µM) against SW620.