A method for the determination of phytol enantiomers in plant-based dairy products was established by gas chromatography-mass spectrometry (GC-MS). The pretreatment process was optimized, and the figures of merit of the proposed method such as linear relationship, precision, spiked recovery, limit of detection (LOD) and limit of quantitation (LOQ) were investigated. Results showed that in the concentration range of 0.0–1.0 μg/mL, the linearity of the method was good (r > 0.999). The LODs of E- and Z-phytanol were 0.03 and 0.04 mg/kg, respectively, and the respective LOQs were 0.09 and 0.10 mg/kg. The recoveries of E- and Z-phytanol in spiked samples were 78.6%–93.5% and 79.5%–94.7%, respectively with relative standard deviations (RSDs) less than 10%. This method is sensitive, accurate and repeatable, and can be used for the determination of phytol enantiomers in plant-based dairy products.