In order to explore the effects of continuous years zero-tillage and rotation on soil nutrient and microorganisms，an experiment of zero-tillage(Z)with crop residues and part.of.straws，which was maintained in the field，and traditional tillage(T)on winter wheat-paddy rice rotation system was conducted for consecutive years in Ningxia Yellow River Irrigation Basin. The methods of conventional soil nutrient determination，metagenomic sequencing，KEGG database and RDA(Redundancy analysis)were used. The experiment focused on soil nutrients，soil microbial communities and their metabolic pathways，and soil enzymes. The results showed that the abundance of soil microbial population structure in 0-20 cm soil was changed in different growth stages of crops. The abundance of Proteobacteria and Acidobacter in the first core population was the highest，showing an increasing trend. However，the second core population，the abundance of Actinobacteria and Chloroflexi showed a decreasing trend. The treatment of rotation and zero-tillage for continuous years increased the contents of urease，sucrase protease and catalase increased than treatment of traditional tillage by 4.9%，22.8% and 21.7%，respectively. The correlation between soil enzymes and crops treated with zero-till rotation was better than treatment of traditional tillage rotation in most growth stages. Meanwhile，the contents of organic matter，total nitrogen，total phosphorus，hydrolyzable nitrogen and available phosphorus in zero-tillage(Z)4 were increased than traditional tillage (T)4 by 27.7%，20.3%，16.1%，30.8% and 19.3%，respectively. However，the difference of soil microbial metabolic pathway between treatments of Z and T was mainly represented by amino acid pathway. The activation degree of most amino acid pathways of Z was significantly higher than T at the first stage (wheat jointing stage) and at the third stage (rice booting stage). In the treatment Z，the Nitrospira and the Anaromyxobacter were more positively correlated with contents of the total potassium，available potassium，organic matter，total nitrogen and hydrolyzable nitrogen. Whereas，the Sphingomonas was more positively correlated with available phosphorus content only. The results also suggested that the correlation between treatment Z and soil enzyme was better than treatment T in most crop growth stages. In conclusion，the fundamental reason for improving soil fertility was maintaining crop residues and straws in the field for many years，provided more “food” for microorganisms，as well as reduced the disturbance to the living environment of soil microorganisms in treatment Z. However，the driving force factors to improve the fertility of soil were that，Proteobacter，Acidobacter and other core dominant bacterial populations in the soil of reasonable rotation system with zero tillage，as well as the catalytic effect of soil enzymes，were better than the traditional tillage，which jointly promoted the transformation and circulation of soil organic matter and soil nutrients. Kay words:zero-tillage and rotation；soil nutrient；soil enzyme；metagenomic sequencing；microbial community structure；redundancy analysis (RDA)