Knowledge of tree biomass allocation is fundamental for estimating forest acclimation and carbon stock for global changes in the future. Optimal partitioning theory (OPT) and allometric partitioning theory (APT) are two major patterns of biomass allocation, and occurrences have been tested on taxonomical, ontogenetic, geographic and environmental scales, showing conflicting results and unclear ecophysiological mechanisms. Here, we examine the biomass allocation patterns of two young poplar (Populus) clones varying greatly in drought resistance under different soil water and nitrogen availabilities and the major physiological processes involved in biomass partitioning. We found that Biyu, a drought-sensitive hybrid poplar clone, had significant relations among biomass of leaf, stem and root, showing allometric partitioning. Xiaoye, a drought-tolerant poplar clone native to semi-arid areas, on the contrary, showed tightly regulated biomass allocation following optimal partitioning theory. Biyu had higher nitrate reductase activity in the fine roots, while Xiaoye had higher nitrate reductase activity in the leaves. Biochemical analyses and measurements of fluorescence and gas exchange showed that Xiaoye maintained more stable chloroplast membranes and photosystem electron flow, showing higher water use efficiency and a higher resistance to drought. A nitrogen addition could improve leaf photosynthesis and growth both in Biyu and Xiaoye seedlings under drought conditions. We concluded that the two poplar clones showed different biomass allocation patterns and suggest that the site of nitrate assimilation may play a role in biomass partitioning under varying water and nitrogen availabilities.