In order to explore the most suitable water and nitrogen system in salinized farmland under the condition of subsurface drainage, a 2-year field experiment was carried out in the hidden pipe layout area of Hetao irrigation district. In the experiment, we set three irrigation levels, including low water (120 mm, I1), medium water (210 mm, I2) and high water (330 mm, I3) as well as three nitrogen levels of low nitrogen (0 kg/hm², N1), medium nitrogen (105 kg/hm², N2) and high nitrogen (210 kg/hm², N3). The effects of different water and nitrogen combinations on soil desalination rate, water and nitrogen utilization efficiency, yield and quality of sunflowers were analyzed. The results showed that under the condition of subsurface drainage, the desalination effect of I3N2 treatment was the best, with an average increase of 5.82% in desalination rate compared to other water nitrogen treatments. Under high water (high nitrogen) conditions, the yield increased with the increasing of nitrogen application amount (irrigation amount), among which the yield of high water and high nitrogen (I3N3) was the highest, with an average of 5 129.72 kg/hm². Under the same irrigation amount, the utilization efficiency of irrigation water was the highest at high nitrogen application (N3), and the higher the nitrogen amount, the lower the productivity of fertilizer. Under low water (I1) and medium water (I2) conditions, high nitrogen (N3) level was the most conductive for synthesis of seed protein and essential amino acid. Under the conditions of high water (I3), medium nitrogen level (N2) was beneficial to the synthesis of seed protein and essential amino acids, while low nitrogen level (N1) was most beneficial to the synthesis of seed crude fat. At each irrigation level, the contents of protein and essential amino acid in medium water (I2) and high water (I3) treatments were generally higher than those in low water (I1) treatments, while the content of crude fat was generally lower than those in low water (I1) treatments. Based on principal component analysis and membership function comprehensive evaluation, it was found that high water and medium nitrogen treatment (I3N2), with an irrigation amount of 330 mm and a nitrogen amount of 105 kg/hm², was the appropriate combination of water and nitrogen in subsurface farmland. The results could provide a theoretical basis for the formulation of scientific water and nitrogen system in the subsurface farmland in Hetao irrigation district.