The composition and form of selenium in the soil have significant effects on the selenium content of crops. In this study, we investigated the selenium absorption pathway in plants by studying the interaction between nitrogen fertilizer and soil selenium. Our results showed that the selenium concentration enrichment factors (CEF) varied within the same region due to nitrogen fertilizer application, where they ranged from 1.33 to 5.02. The soil selenium flow coefficient (mobility factor, MF) increased with higher nitrogen application rates. The sum of the MF values for each soil layer treated with nitrogen application rates of 192 kg hm-2 and 240 kg hm-2 was 0.70, which was 64% higher than that for the control group with no nitrogen application. In the 0-20 cm soil layer, the highest summed water-soluble and exchangeable selenium and relative percentage of total selenium (12.45%) was observed at a nitrogen application rate of 240 kg hm-2. In the 20-40 cm soil layer, the highest relative percentage content of water-soluble and exchangeable selenium and total selenium (12.66%) was observed at a nitrogen application rate of 192 kg hm-2. Experimental treatment of black wheat with various concentrations of sodium selenite showed that selenium treatment at 50 μmol L-1 significantly increased the reduced glutathione (GSH) levels in the leaves and roots of seedlings, where the GSH contents increased by 155.4% in the leaves and by 91.5% in the roots. Further analysis of the soil-black wheat system showed that nitrogen application in selenium-rich areas affected the soil selenium flow coefficient and morphological composition, thereby changing the enrichment coefficient for leaves (0.823), transport capacity from leaves to grains (-0.530), and enrichment coefficient for roots (0.38). These changes ultimately affected the selenium concentration in the grains of black wheat.