Abstract: The development of spike traits in graminaceous plants is unbalanced, and so is that of Coix lacryma-jobi L. Due to the sequential order of glume differentiation, the process of grouting and development between grains in different parts of the plant are not synchronized, which ultimately leads to inconsistency in maturity. The differences between the strong and weak grains are highlighted with the increase in the number of secondary pedicels, thus limiting the further exploitation of the yield potential of Coix lacryma-jobi L. Nitrogen, phosphorus, and potassium fertilizer rationing is an effective way to narrow the differences in grouting firming characteristics between seed parts by comparing the effects of different N, P, and K fertilizers on the dynamics of grain weight gain in different parts of Coix lacryma-jobi L., the parameters of the grouting characteristics, the fruiting characteristics, and the effect of fertilizers, and to explore the optimal fertilization of Coix lacryma-jobi L. to provide theoretical and technical support for this high-efficiency fertilization technology model. Taking ‘Guiyi No.1’ as the material, Richards’ equation was applied to study the grouting process of grains in five parts of Coix lacryma-jobi L. (upper, middle, basal 1, basal 2 and basal 3 parts) under different nitrogen (N), phosphorus (P) and potassium (K) fertilizers in ‘3414’ design. The results showed that 1) the application of N, P, and K fertilizers could prolong the number of days required to reach the maximum grouting rate and the active seed-filling period of grains in the upper, middle, basal 1, basal 2, and basal 3 parts of Coix lacryma-jobi L., increase the grain weight at the maximum grouting rate; the average grouting rate and the maximum seed-filling rate, which would, in turn, improve the characteristics of Coix lacryma-jobi L. fruiting. 2) N, P, and K fertilizers significantly increased the grain weight in the middle and basal parts of Coix lacryma-jobi L., with N>K>P among single-factor fertilizer effects and PK>NP>NK among two-factor fertilizer interactions. However, excessive application of N, P, and K fertilizers decreased the grain weight, and the fruiting characteristics were significantly deteriorated. 3) Correlation analyses showed that the thousand-grain weights of grains in the upper, middle, basal 1, basal 2, and basal 3 parts of the plant were positively correlated with grain firmness, fullness, average grouting rate, and maximum seed-filling rate. 4) Fitting the equation of the effect of fertilizer on the thousand-grain weight of Coix lacryma-jobi L., the optimal recommended fertilizer application ranges for it were 135.51–270.99 kg·hm^–2, 75.00–150.50 kg·hm^–2, and 56.25–112.51 kg·hm^–2, for N, P₂O₅, and K₂O, respectively. Nitrogen, phosphorus, and potassium fertilizers significantly affect different parts of Coix lacryma-jobi L. grain filling and fruiting characteristics, and the appropriate proportion can not only significantly promote grain filling and reduce the differences between parts, but can also improve the fruiting rate and grain weight. In the production of Coix lacryma-jobi L., nitrogen fertilizer had the greatest influence on grain filling and fruiting characteristics of Coix lacryma-jobi L., potassium fertilizer had the second largest influence, and phosphorus fertilizer had the smallest influence.