Wolfiporia cocos is an edible fungus commercially cultivated in Asia. To investigate metabolic changes of W. cocos mycelia under both light and dark culture conditions, gas chromatography mass spectrometry (GC-MS) and high-performance liquid chromatography (HPLC) analyses were performed. In terms of the total amount of sugars, alcohols, amino acids, organic acids, fatty acids, and purines, there no significant differences between the W. cocos mycelia cultivated under light (L) or dark (D) conditions (p < 0.05). However, there were some differences with respect to the production of particular sugars and proteins. The levels of trehalose (L: 17.2 ± 0.3% vs. D: 13.9 ± 1.6%), maltose (L: 0.9 ± 0.1% vs. D: 0.3 ± 0.1%), turanose (L: 0.7 ± 0.2% vs. D: 0.1 ± 0.1%), glutamine (L: 1.6 ± 0.3% vs. D: 0.7 ± 0.2%), and proline (L: 0.3 ± 0% vs. D: 0.1 ± 0%) were all significantly higher under light condition (p < 0.05). In contrast, the levels of galactose (L: 13.7 ± 1.2% vs. D: 17.6 ± 2.0%), aspartic acid (L: 0.6 ± 0.1 % vs. D: 0.9 ± 0.1%), cystathionine (L: 0.6 ± 0.1% vs. D: 0.8 ± 0 %), and malic acid (L: 0.7 ± 0.1% vs. D: 1.2 ± 0.1%) were higher under the dark condition. It is worth noting that the amount of pachymic acid, a pharmaceutically active compound of W. cocos, was 1.68 times greater under the light condition (p < 0.05).