Background <p>Nitrate (represented by NN or NO₃⁻-N) and ammonium (represented by AN or NH₄⁺-N) are the two predominant nitrogen (N) forms utilized by plants; however, the physiological mechanisms underlying citrus response to different N forms are still poorly understood. In this study, seedlings of two citrus varieties (<i>Citrus reticulata</i> Blanco cv. Lugan and <i>Citrus sinensis</i> (L.) Osbeck cv. Xuegan) were cultivated under two N forms (NN and AN, at 4 mmol L^− 1) to investigate their ultrastructural, physiological, and biochemical characteristics.</p> Results <p>Compared with AN treatment, NN treatment significantly promoted plant growth by regulating the physiological and morphological characteristics of roots and leaves. Under AN conditions, there was an excessive accumulation of free amino acids and soluble proteins in both leaves and roots, which suppressed the activity of N assimilation enzymes and consequently reduced plant N uptake. Furthermore, AN treatment inhibited photosynthetic performance by decreasing chlorophyll content, damaging chloroplast structure, and disrupting photosynthetic electron transport chain. Consequently, this led to the accumulation of non-structural carbohydrates in both leaves and roots, ultimately affecting the morphogenesis of citrus plants. Additionally, AN treatment induced an oxidative stress response, increasing malondialdehyde (MDA) levels and eliciting an antioxidant response in citrus seedlings. Moreover, based on measured physiological parameters, principal component analysis showed an obvious separation between AN and NN treatments.</p> Conclusions <p>Our findings demonstrated that NN supply enhanced plant growth owing to the improved coordination of carbon and N metabolism in citrus plants, thereby providing a basis for optimizing N management strategies in sustainable citrus production.</p>