Alkylated polycyclic aromatic hydrocarbons (APAHs) are the main components of polycyclic aromatic hydrocarbons (PAHs) in petroleum-contaminated waters. In our study, three kinds of green microalgae (Pseudokirchneriella subcapitata, Chlorella vulgaris and Scenedesmus obliquus) were shown to degrade six kinds of methylphenanthrenes (1-methylphenanthren, 2-methylphenanthrenem, 3-nmmethylphenanthrene, 4-methylphenanthren, 9-methylphenanthrene and 3,6-dimethylphenanthrene) with different degrading abilities. Among the six methylphenanthrenes, 99.8% of 1-methylphenanthrene (1-MP) was removed and 75.6% of 3,6-dimethylphenanthrene (3,6-DMP) was removed by P. subcapitata after 7 days of incubation. The metabolites of 1-MP and 3,6-DMP were identified by gas chromatograph-mass spectrometer (GC-MS). Six metabolites of 1-MP and one metabolite of 3,6-DMP were found, they were all monohydroxylated methylphenanthrenes. The -OH group was added to either methyl-group or benzene ring through the monooxygenase system, and the methyl-group attack was the main pathway. This research increases our knowledge of the degrading ability of APAHs by green microalgae and offers information for the bioremediation of APAHs. Quantum chemical calculation was conducted to elucidate the biodegradation metabolites of methylphenanthrene by green microalgae, which is a helpful tool in the bioremediation of environmental pollution.