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The species <i>Pseudogymnoascus</i> is known as a psychrophilic pathogenic fungus with a ubiquitous distribution in Antarctica. Meanwhile, the study of its secondary metabolites is infrequent. Systematic research of the metabolites of the fungus <i>Pseudogymnoascus</i> sp. HSX2#-11, guided by the method of molecular networking, led to the isolation of one novel polyketide, pseudophenone A (<b>1</b>), along with six known analogs (<b>2</b>–<b>7</b>). The structure of the new compound was elucidated by extensive spectroscopic investigation and single-crystal X-ray diffraction. Pseudophenone A (<b>1</b>) is a dimer of diphenyl ketone and diphenyl ether, and there is only one analog of <b>1</b> to the best of our knowledge. Compounds <b>1</b> and <b>2</b> exhibited antibacterial activities against a panel of strains. This is the first time to use molecular networking to study the metabolic profiles of Antarctica fungi.