In order to study the effects of water stress and different levels of nitrogen fertilizer on grian yield and accumulation macronutrients included: nitrogen, phosphorus and potassium and micronutrient included: iron, zinc, manganese and copper, oil, protein and thymoquinone contents in seed of black cumin, a field experiment was conducted as split plot design with three replications at Agricultural Research Station, Zahak, Zabol during growing season of 2010-2011. Water stress treatments included: W1= control, W2= no irrigation at stem elongation stage to flowering, W3= irrigation at flowering stage until the beginning of grain filling and W4= no irrigation at flowering and grain filling as the main plots and four levels of nitrogen application fertilizer, including N1= control or without any fertilizer consumption, N2= 30 kg N/ha, N3= 60 kg N/ha and N4= 90 kg N/ha in sub plot. Results showed that water stress had significant effect on the grain yield and accumulation of macro and micronutrient in the seed of Black Cumin. Except for and iron, the highest amounts of nitrogen, phosphorus, potassium, manganese, copper and zinc and the lowest amount of grain yield were obtained at W4 treatment and manganese at W3 treatment. In this experiment the interaction effect between stress and nitrogen fertilizer except grain yield and potassium had significant impact on others elements. The results indicated that water stress at flowering and grain filling (W4) stages, the maximum amount of micro and macronutrients in seed was obtained at N1 and N2 nitrogen treatment. Also, water stress and nitrogen treatments increased the percentage of protein, oil and thymoquinone contents of seed, but during the onset of water stress and the use of nitrogen fertilizer, the highest percentage of protein in and thymoquinone were obtained in W4N4.