The experiment of drought treatment of rootstock Poncirus trifoliata (L.) Raf. was carried out by using the method of drought stress and water control (the relative water holding capacity of the control group was maintained at 55% to 65%) on potted. The effects of drought stress on the total nitrogen content of the lateral roots, main roots, stems and leaves of P. trifoliata, as well as the expression of 16 genes related to NRT, NR, NiR, GS, GOGAT and GDH in the lateral roots and leaves of the nitrogen metabolism pathway were analyzed on 7 days, 17 days, 27 days and 37 days after treatment. The results showed that the total nitrogen content in the roots, main roots, stems and leaves of P. trifoliata significantly decreased with the increase of drought time, and the total nitrogen content in the lateral root decreased most significantly.16 genes of nitrogen metabolism in leaves of P. trifoliata can be up–regulated by drought stress, and most of them were increased to the highest level after drought treatment for 27 days, and then decreased with the wilting of leaves. In the lateral roots of P. trifoliata, the expression of 8 genes (NRT1.2, NRT1.7, GS2, NADH–GOGAT2, NADP–GDH, GDH1, GDH2 and GDH3) was induced by drought stress after 27 days treatment and showed up to varying degrees, and there were no significant changes in the expression of 4 genes (NRT1.1, NRT1.5, GS1, NADH–GOGAT3), which were not affected by drought stress, and the other 4 genes (NR, NiR, Fd–GOGAT, NADH–GOGAT1) were significantly down regulated by drought stress.