Cynanchum taiwanianum is an important plant used in traditional medicine. The increasing demand and lack of information regarding its cultivation have become concerns for sustainability. This study examined the effects of nitrogen and potassium fertilization rates on the growth and biosynthesis of main bioactive compounds, including cynandione A and polyphenolic compounds, in field-cultivated C. taiwanianum. Two field experiments were conducted using three levels of nitrogen (N100, N150 and N200) and three levels of potassium (K100, K150 and K200) treatments. The experimental variables were either N or K fertilizer. The results showed that, aside from N200, N and K fertilization significantly increased C. taiwanianum shoot and tuber biomass. High N fertilization resulted in low total phenolic and total flavonoid contents in shoots and tubers, but the effects of K fertilization were minimal. Cynandione A, an important bioactive compound, was only detected in tubers; its content were enhanced with the increasing K fertilization, but reduced with excess N fertilization (N200). Although N and K fertilizers are important for C. taiwanianum tuber production, the yield of cynandione A was associated with K but not N fertilization rates. These results provide some essential information for the optimal production of C. taiwanianum tubers and functional compounds. Further studies are required to examine the mechanism(s) of cynandione A biosynthesis and its compartmentation in plant tissues.