Secondary metabolites have been extensively used in the treatment of various health problems. The role of solvent polarity on the phytochemical isolation and antioxidant capacity of (woad) is elusive. In the present study, 14 solvents with different polarity were used in the extraction and total phenolic and flavonoid content (TPC and TFC) investigation. Ferricyanide, phosphomolybdenum, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) methods were used to calculate and compare the antioxidant/free radical scavenging capacity. Our results showed that solvent polarity greatly affects TPC and TFC yield, which is mainly increasing with increasing solvent polarity index and suddenly decreasing at very high polarity. The comparative results showed that TPC is directly correlated with reducing power, antioxidant, and free radical scavenging capacity. Taken together, we conclude that different woad plant parts contain different level of secondary metabolites with a specific polarity that requires a particular solvent with an appropriate polarity index for the extraction. The identification of these biologically active crude extracts and fractions are very important for the basic biological sciences, pharmaceutical applications, and future research for HPLC based active compounds isolation.