Background: The role of macro and micro nutrients have been reported in various plant. However, in perennial trees, the function of multiple elements to different genotypes remain to be elucidated. This study aimed at deciphering the genetic architecture of physiological differences under different nutrient levels between the high- and low-growth genotypes. Results: Our results showed that growth traits of both genotypes at nutrient starvation treatment was much lower than that at nutrient abundant treatment, indicating that nutrient is essential for plant growth. However, tree height, crown width, and fresh weight of different tissues of ZQUA44 were much higher than that of ZQUB15 at the three nutrient levels, implicating the genetic basis of different trees is another factor that varied the phenotypic performance. The differentially expressed genes (DEGs) were clustered into 6 subclusters depending on different expression pattern. Functional annotation of DEGs from different subclusters showed that DEGs involved in glutathione metabolism, flavonoid biosynthesis and stilbenoid, diarylheptanoid and gingerol biosynthesis may responsible for nutrient starvation across different genotypes, while DEGs involved in carotenoid biosynthesis and starch and sucrose metabolism may have diverse function in different genotypes. The DEGs encoding MYB_related may responsible for nutrient deficiency of all the genotypes, while B3 may play different functions in different genotypes. Conclusion: Our results demonstrate that different genotypes may form different metabolic pathways to coordinate plant keeping survival when they face abiotic stresses. Furthermore, we elucidate DEGs that may widely responsible for nutrient deficiency in different treatments and DEGs that play different functions in different genotypes. Finally, our funding provide adequate nutrient supply for Eucalyptus.