Previous studies have shown that there are significant sexual differences in the physiological responses of Torreya grandis to environmental stress. However, little is known about its sex-specific differences in response to salt stress against the background of nitrogen (N) deposition. In this experiment, two-year-old male and female T. grandis seedlings were used as experimental materials and exposed to moderate salt conditions and different N levels to study the effects of nitrogen addition and salt stress on the chlorophyll content, chlorophyll fluorescence parameters, antioxidant system, and leaf stoichiometry of T. grandis seedlings. With the increase in nitrogen content, the contents of proline, malondialdehyde, superoxide anion, and H2O2 in the leaves of T. grandis seedlings under salt conditions gradually increased. The contents of these four metabolites in the leaves of male T. grandis seedlings were almost all higher than those of the female ones. Compared with the control group, the contents of enzymatic and non-enzymatic antioxidants increased under N addition treatments, especially for the low and moderate N addition groups. The results showed that moderate concentrations of N addition can mitigate the damage caused by salt, while high concentrations of nitrogen do not. Under conditions of salt and nitrogen addition, female T. grandis seedlings outperformed male ones, as evidenced by their higher photosynthetic pigment content, enhanced antioxidant enzyme activity, reduced accumulation of intracellular cytotoxic metabolites, and higher carbon and nitrogen content in their leaves compared to those of male seedlings. The findings of this research will contribute to our understanding and offer a theoretical foundation for the cultivation of T. grandis seedlings in environments with nitrogen deposition and salinization.