Abstract: Flaxseed has been widely used in a variety of applications for over 100 years, due to its reputation for cosmetic and health benefits. The germination may be enhanced the efficiency of flax seed, but there is a lack of scientific evidence supporting this inference. In order to clarify this problem, the phytochemical composition of flaxseed with different germination time (from 0 day to 8 days) was identified by using high performance liquid chromatography-diode array detector coupled with two-stage tandem mass spectrometry (HPLC/MS²). The separation was performed on a Phenomenex ODS C18 column (4.6 mm×250 mm×5 μm), of which 0.2% aqueous acetic acid (V/V) (A) and methanol (B) were used as the mobile phase. The flow rate was 0.75 mL/min. The column temperature was maintained at 25 ℃. The diode array detector (DAD) detection wavelength was set at 280 nm. MS analysis was carried out by the electrospray ionization ion source (ESI) in both positive and negative ion modes. The total flavonoid content (TFC) and the total phenolic content (TPC) in flaxseeds before and after germination were measured by UV spectrophotometric method. Furthermore, the antioxidant activity of flaxseed was evaluated by the ferric reducing antioxidant power (FRAP), DPPH scavenging (DPPH) and oxygen radical absorbance capacity (ORAC) assays. Compared to the non-germinated flaxseeds (0 day), twelve compounds were identified in partially germinated seeds and sprouts (day 1-8), including sucrose, nucleosides, purines and flavonoid. The TFC, TPC and antioxidant activities were found to increase as the flaxseeds germinate. This research shows that germination is a good process to increase the flavonoid content of flaxseeds as well as the antioxidant activity, and it provides a reliable theoretical basis for development of flaxseed as health care products and functional food.