While cotyledon damage is known to impair seedling establishment in desert plants, how increasing nitrogen deposition may mediate these effects remains poorly understood, particularly for species with different root developmental strategies. This study provides the first experimental evidence of the interactive effects of cotyledon damage timing and nitrogen enrichment on two ecologically important Salsola species with contrasting root architectures. We subjected seedlings of S. heptapotamica (with rapid root development) and S. ruthenica (with slower root development) to sequential cotyledon removal (0, 1 or 2 cotyledons removed at 1, 3, 5, and 7 days post-emergence) combined with four nitrogen concentrations. Our key novel findings reveal that: (1) nitrogen application could not compensate for cotyledon loss in terms of seedling survival for either species, challenging the assumption that nutrient enrichment necessarily mitigates early damage; (2) nitrogen differentially enhanced growth traits in S. heptapotamica but not S. ruthenica, highlighting species-specific responses linked to their root developmental strategies; and (3) the timing of damage (3rd vs. 5th day) mediated nitrogen effects in S. ruthenica, suggesting critical windows for nutrient intervention. These results advance our understanding of how anthropogenic nitrogen deposition may alter regeneration dynamics in arid ecosystems, with important implications for predicting vegetation responses to global change.