The leaf nitrogen (N) content (NL) and its allocation are major factors that determine the photosynthetic characteristics and photosynthetic N-use efficiency (PNUE) of tree species. In this study, we investigated the allocation of NL to the photosynthetic apparatus (NP) and its effects on the photosynthetic characteristics and PNUE of three tropical tree species (Magnolia montana Blume, Swietenia macrophylla King, and Acacia mangium Willd), which were grown in western Java, Indonesia. A. mangium (the only N-fixing species among three studied species) exhibited a greater NL and NP than other two species, resulting in higher capacities of photosynthetic parameters such as the light-saturated photosynthetic rate (Pmax), maximum carboxylation rate (VCmax), and maximum electronic transport rate (Jmax). However, S. macrophylla and A. mangium displayed a similar fraction of leaf N allocated to NP (NP/NL) and showed a higher NP/NL ratio than M. montana. Accordingly, S. macrophylla presented a higher PNUE than M. montana. Although A. mangium exhibited a similar PNUE to S. macrophylla, A. mangium showed a higher NL than the other two species, which resulted in a lower PNUE at a given NP. In addition, stomatal conductance was positively correlated with PNUE, but the slopes of the correlations between species presented a negative relationship with the leaf mass per area (LMA), which caused a longer pathway to the photosynthetic apparatus. Our results suggested that the variation of PNUE between species was affected by various factors, including the fraction of NL allocated to NP and morphological characteristics such as LMA.