[Objective] The objective of this study was to assess the effect of fermented cotton stalk in the diet on rumen microflora of weaned lambs by using high-throughput sequencing technology.[Methods] Thirty Hu sheep were selected and randomly divided into three groups according to different proportions of fermented cotton stalk in the diet:the control (S0), 50% fermented cotton stalk (S50) and 100% fermented cotton stalk (S100), six sheep were randomly slaughtered in each group to analyze their growth performance, rumen fermentation parameters and microflora analysis.[Results] Feeding 50% fermented cotton stalk can significantly improve the daily gain and slaughter rate of lambs (P<0.05). Bacteroidetes and Firmicutes are the dominant phylum in the rumen, Prevotella and Unclassified Bacteroidales are the dominant genus of the rumen of the lambs. Adding 100% fermented cotton stalk to the diet could significantly reduce both the diversity of rumen microflora and the relative abundance of Unclassified Bacteroides and BF311 (P<0.05). Three metabolic pathways significantly increased as the proportion of fermented cotton stalk increased (P<0.05).[Conclusion] Feeding 50% fermented cotton stalk had little effect on the structure and function of rumen microflora while increasing daily weight. In production practice, the content of fermented stalk should be lower than 50%.