A novel hydroanthraquinone possessing an unprecedented hexacyclic spiro-fused ring system, anthrininone A (1), and two new anthraquinones with a 4,5-disubstituted butylaminolate unit, anthrininones B and C (2 and 3), together with six known analogues including 6-O-methylalaternin (4) and so on, were obtained from the deep-sea derived fungus Alternaria tenuissima DFFSCS013. Their structures were determined by spectroscopic methods, and the absolute configurations were further determined by single crystal X-ray diffraction analysis for 1 and quantum chemical calculations for 2 and 3, respectively. Compounds 1–4 had significant inhibition activity against indoleamine 2,3-dioxygenase 1 (IDO1), and 2–4 also exhibited selective inhibition activity against different protein tyrosine phosphatases. In addition, 1 could obviously stimulate intracellular calcium levels at a concentration of 10 μM. Their structure–bioactivity relationship was also discussed.