A pot experiment with “3414” incomplete orthogonal design was performed using foxtail millet cultivar Jingu 21 as material to study the effects of N, P, and K fertilization rates under different water supply levels. The results indicated that when drought stress was maintained at a mild level, the treatments of N (100, 150 mg N·kg^-1), P (87, 130.5 mg P·kg^-1) and K (249, 373.5 mg K·kg^-1) applications significantly improved the physiological characteristics of foxtail millets, the contents of soluble sugar and soluble protein as well as the enzyme activities of POD, SOD and CAT in the foxtail millet seedlings were apparently increased, and the MDA contents were remarkably decreased. However, the physiological performance of foxtail millets exhibited better effects when the rates of N (100, 150 mg N·kg^-1), P (87 mg P·kg^-1), and K (124.5, 249 mg K·kg^-1) were respectively supplied under heavy drought stress. Our data showed that when the plants were subjected to mild or heavy drought stress, the mixed application of N, P and K exhibited better reciprocation effects on the growth of foxtail millet at seedling stage compared to the single application of N, P, or K. This study suggested that under heavy drought stress, although applications of N, P and K could promote the foxtail millet growth by enhancing the tolerance of plants to drought stress, the appropriate ranges of fertilization were narrow, and excessive applications of fertilizers would cause physiological damages on the growth of foxtail millet.