The aim of this study was to evaluate effects of nitrogen and flower pruning on morphological characteristics, seed yield and silymarin content of Milk thistle. The experiment was conducted as split plot, in which the main factor was nitrogen at three levels of 0 (N-0), 50 (N-50) and 100 (N-100) kg/ha, and the sub factor was pruning at three levels; without pruning (P-0), pruning of one flower (P-1) and two flowers (P-2). Results indicated that the interaction between nitrogen and flower pruning had significant effect on plant height, as maximum and minimum plant height were obtained from N100P2 and N50P1 treatments, respectively. The highest and the lowest seed yield were found in the N50P2 and N0P0 treatments, respectively. Number of seeds per capitula was decreased by increasing the flower pruning. Capitula diameter was also increased by increasing N levels. The interaction of nitrogen levels and flower pruning had significant effect on content of silymarin, silybin, silicristin, and silydianin. The highest content of silymarin, silybin B, silydianin and silycristin A were observed in the N50P2 treatment and the lowest were observed in the N0P1, N0P0, N0P0 and N0P0 treatments, respectively. No significant effect was observed for silybin content by nitrogen levels and flower pruning, and for silycristen content by nitrogen levels.