The novel diketopiperazine alkaloid toxicocladine A (1), two new natural products cyclo(L-Phe-AAla) (2) and cyclo(L-Tyr-AAla) (3), and three known compounds protocatechuic acid (4), protocatechuic acid methyl ester (5) and ergosterol peroxide (6), were isolated from the fungus Toxicocladosporium sp. CYH-18 collected from the Haima cold seep. The structures and absolute configurations of the compounds were determined via NMR, MS, optical rotation, and X-ray diffraction analysis and by comparison with the literature. Structurally, compound 1 was a diketopiperazine with an unprecedented methylene sulfide bridge between C-5 and C-8, while compounds 2 and 3 were diketopiperazines with terminal olefins. Compounds 4 and 5 showed antioxidant activity. Compound 6 displayed antibacterial activity against Bacillus subtilis and Exiguobacterium profundum.