Recently, polycosanol products have been actively introduced into the domestic market based on their potential biological activity. The analytical procedures of polycosanol, which determine the TMS derivatives of each polycosanol with GC-FID, were presented for inspection of standards. However, the conventional procedures are not readily applicable to polycosanol emulsion which is prepared by mixing polycosanol and water together with emulsifiers because of their interferences. Therefore, the quantitative analytical procedure of polycosanol emulsion with GC-MS at selected ion monitoring mode was proposed and its validity was inspected for standardization. The analysis of polycosanol standards according to the proposed procedure showed the following values: 90.5% for reproducibility; 0.48-5.83% for the RSD; 0.000479-0.001314 μg/μL for the LOD; 0.001452-0.003983 μg/μL for the LOQ; 80.38-108.98% for accuracy; and 0.01-4.88% for the coefficients of variation. The average reproducibilities of polycosanol emulsions according to the current procedure were 87.43±4.48% and 88±2.2%, respectively, which were within the 80-120% range of the designated amounts. Therefore, it was found that the proposed analytical procedure with GC-MS at SIM mode in this study would be promising for the accurate quantitative analysis of polycosanol emulsion.