Nitrogen (N), phosphorus (P), and potassium (K) are three crucial factors that affect the yield and quality of waxy sorghum (Sorghum bicolor L. Moench), which is used in liquor production. To optimize the fertilization measures for high yield and high amylopectin/total starch ratio in the Hongliangfeng 1 waxy sorghum cultivar, 23 treatments with five levels of three variables (N, P, and K fertilizers) were arranged in a quadratic orthogonal rotation combination design. Results showed that N fertilizer had significant effects on both the yield and amylopectin/total starch ratio, whereas P fertilizer significantly affected only the yield. K fertilizer and the interactions of the three studied factors showed no significant effects on the yield or amylopectin/total starch ratio. The effects of the three studied factors on yield and the amylopectin/total starch ratio were ranked as N fertilizer > P fertilizer > K fertilizer and N fertilizer > K fertilizer > P fertilizer, respectively. Both yield and amylopectin/total starch ratio increased and then decreased with increasing application of N, P, and K fertilizer. The optimal fertilization combination for a yield greater than 5800 kg ha⁻¹ and an amylopectin/total starch ratio greater than 91% was 262.29–324.30 kg ha⁻¹ N, 114.07–139.26 kg ha⁻¹ P₂O₅, and 230.22–369.28 kg ha⁻¹ K₂O.