Reducing plant spacing and pruning Jatropha hybrids may increase yield. The study aimed to investigate the effect of reduced plant spacing on yield productivity, assess pruning tolerance, and discover the relationship between yield and growth traits of Jatropha hybrids. Fourteen Jatropha hybrid genotypes evaluated yield with narrow and standard plant spacing for two years. After the first year, the Jatropha hybrid plants were hard-pruned and allowed to regrow in the second year. It found that although narrower plant spacing might reduce Jatropha hybrid growth and yield per plant, increasing plant density by reducing plant spacing could increase fruit yield, seed yield, and oil yield by up to 65.46%, 64.73%, and 63.25%, respectively, when compared to standard spacing. Furthermore, hard pruning could improve the growth of Jatropha hybrids, and pruning tolerance varied between genotypes. Under narrow spacing, KUJL110 and KUJL70 had the highest yields after pruning, and KUJL110, KUJL30, and KUJL23 had the highest pruning tolerance index (PTI). It discovered a correlation (ranging from 0.49** to 0.86**) between yield traits and plant height, canopy width, and the number of secondary branches. Additionally, a correlation (ranging from 0.51** to 0.83**) was found between oil content and shelling, as well as 100 seed weight. As a result, these traits may serve as an indirect tool for selecting Jatropha genotypes with high-yield traits.