The application of fertilizer greatly increased crop yield worldwide in the past half-century. However, increasing farming cost and energy consumption, especially threatening environments of over-applied fertilizer strongly demands crop varieties with high nutrient use efficiency. The dynamic chromatin state is key to transcriptional regulation, yet the epigenetic transition in diverse nitrogen conditions remains largely uncharted. Here, we drew the chromatin landscape dynamics of three tissues between different Nitrogen conditions in two nitrogen use efficiency (NUE) diverse wheat cultivars (KN9204 and J411). Epigenomic analysis revealed distal regulatory regions exhibit a clear cultivar specificity and are crucial for agricultural trait divergence between KN9204 and J411. For nitrogen metabolism genes (NMGs), the divergence of transcriptional levels regulated by chromatin status is much higher than genetic variations. Such epigenetic difference leads to an altered nitrogen metabolism pathway between KN9204 and J411, eventually affecting plant morphology and yield output under low nitrogen conditions. In particular, we found that dramatic change of H3K27ac pattern in KN9204 and J411 differs in adaptation to low nitrogen conditions, with altered root growth outcome. In addition, genetically impaired histone methyltransferase SWN induced H3K27me3 change, which had significantly improved root growth under low nitrogen conditions. Together, our results show that epigenome varied in the cultivar and low nitrogen adaptation difference, which plays a vital role in low nitrogen adaptation and also provides a new perspective for NUE improvement of wheat.