The impact of nitrogen (N) and phosphorus (P) on the physiological and biochemical processes crucial for tree seedling growth is substantial. Although the study of plant hydraulic traits in response to N and P is growing, comprehensive research on their combined effects remains limited. Malus sieversii, a key ancestral species of modern apples and a dominant species in Xinjiang’s Tianshan wild fruit forest, is witnessing a decline due to climate change, pests and diseases, compounded by challenges in seedling regeneration. Addressing this, a four-year study was conducted to determine the optimal fertilization method for it. The experiment explored varying levels of N (N10, N20, N40) and P (P2, P4, P8), and their combined effects (N20Px: N20P2, N20P4, N20P8; NxP4: N10P4, N20P4, N40P4), assessing their impact on gas exchange, hydraulic traits, and the interplay among functional traits in Tianshan Mountains’ M. sieversii seedlings. Our study revealed that all nitrogen treatments enhanced gas exchange, while phosphorus addition negatively impacted it. N10 significantly increasing leaf hydraulic conductivity. All phosphorus-inclusive fertilizers adversely affected hydraulic conductivity. P8, N20P4 and N20P8 notably increased seedlings’ vulnerability to embolism. Seedlings can adaptively adjust multiple functional traits in response to nutrient changes. The research suggests N10 and N20 as the most effective fertilization treatments for M. sieversii seedlings in this region, while fertilization involving phosphorus is less suitable. This study contributes valuable insights into the specific nutrient needs of it, vital for conservation and cultivation efforts in the Tianshan region.