Organic manure and biochar amendments have been used in agriculture to improve soil fertility and enhance crop productivity. Plant roots play an important role in the functionality of individual plants, and although the addition of organic manure and biochar reportedly affect roots, it remains unclear how root morphology and physiology respond. We conducted a field experiment to test the hypothesis that organic manure combined with biochar amendment could also enhance the productivity of continuous cropping systems in Xinjiang cotton plantations. Different levels of organic manure and biochar were applied. Organic manure and biochar significantly affected root morphology and physiology by improving soil nutrients. In the absence of biochar, organic manure amendment increased Root TTC reducing capacity, glutamine synthetase and nitrate reductase activity. Furthermore, morphological and physiological parameters peaked with 6% organic manure combined with 1% biochar. A significant increase in root physiology was recognized with an increase in soil nutrient content at the bud stage and a negative relationship between root physiology and soil total K content at the harvesting stage. Thus, our results indicate that organic manure combined with biochar positively influenced cotton roots, and therefore should be used to improve root health in continuous cropping systems.Xinjiang has abundant land resources, and its climate has low precipitation, high levels of sunshine and large temperature difference between day and night. When combined with the large-scale application of drip irrigation and mechanized cotton planting, this ensures the higher economic benefit of cotton in Xinjiang compared with other inland cotton producing areas. Compared with other crops such as safflower, maize, and wheat, cotton has outstanding advantages and stable benefits including high profit, advantage of planting technology and preferential policy 1 . By 2016, the cotton planting area and cotton yield in Xinjiang accounted for 53.97% and 67.3% of the whole country, respectively. Owing to the slow process of agricultural industrialization, large area of the land involved, short period of contracts, and driven by economic interests, continuous cropping is widespread in Xinjiang 2 . 73.1% of cotton fields in Xinjiang have been continuously cropped for more than five years 3 .In continuous cropping systems, demand for nutrients causes imbalances in soil nutrients in cotton fields, affects the growth, nutrient uptake, and utilization efficiency of roots, and ultimately reduces yield. Previous studies have reported a significant correlation between cotton yield and soil N, C, and P quality ratios during continuous cropping 4 . Soil organic matter, available P, and available K, and trace elements, including available Mn, available Fe, and available Cu exhibit different trends and degrees of change, which leads to imbalances in soil nutrients in cotton fields 5 . In addition, the yield of cotton fields continuously cropped for the same number of years...