Carbon dioxide (CO2) enhancement (eCO2) and N addition (aN) have been shown to increase net primary production (NPP) and to affect water-use efficiency (WUE) for many temperate ecosystems, but few studies have been made on subtropical tree species. This study compared the responses of NPP and WUE from a mesocosm composing five subtropical tree species to eCO2 (700 ppm), aN (10 g N m−2 yr−1) and eCO2 × aN using open-top chambers. Our results showed that mean annual ecosystem NPP did not changed significantly under eCO2, increased by 56% under aN and 64% under eCO2 × aN. Ecosystem WUE increased by 14%, 55%, and 61% under eCO2, aN and eCO2 × aN, respectively. We found that the observed responses of ecosystem WUE were largely driven by the responses of ecosystem NPP. Statistical analysis showed that there was no significant interactions between eCO2 and aN on ecosystem NPP (P = 0.731) or WUE (P = 0.442). Our results showed that increasing N deposition was likely to have much stronger effects on ecosystem NPP and WUE than increasing CO2 concentration for the subtropical forests. However, different tree species responded quite differently. aN significantly increased annual NPP of the fast-growing species (Schima superba). Nitrogen-fixing species (Ormosia pinnata) grew significantly faster only under eCO2 × aN. eCO2 had no effects on annual NPP of those two species but significantly increased annual NPP of other two species (Castanopsis hystrix and Acmena acuminatissima). Differential responses of the NPP among different tree species to eCO2 and aN will likely have significant implications on the species composition of subtropical forests under future global change.