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To clarify the changes of root traits, soil biological characteristics and yield after applying fertilizers for 39 years, a long-term located fertilization experiment (1981-) was conducted. Compared to NPK (inorganic fertilizer) and M (organic fertilizer), 0.8NPKM (80% of NPK plus 80% of M) and 0.5NPKM (50% of NPK plus 50% of M) obviously improved root traits. The number of bacteria, fungi, actinomycetes in 0.8NPKM and 0.5NPKM were significantly higher than that in NPK, M and CT (no fertilizer). Compared to NPK, M increased soil microbial quantity. Soil microbial biomass carbon and nitrogen, organic carbon and total N in M were higher than that in NPK. The activities of phosphatase, dehydrogenase and urease in M were significantly higher than that in NPK. Compared to NPK and M, 0.8NPKM and 0.5NPKM enhanced above-mentioned soil enzymes activities. The differences in wheat and maize yields between 0.5NPKM and 0.8NPKM were insignificant, and the harvest index in 0.5NPKM was the highest. Soil microbial quantity, microbial biomass carbon and nitrogen were positively correlated with enzymes activities and root traits. Thus, appropriate combined application amount of organic and inorganic fertilizer might be an effective way to improve root traits, rhizosphere soil micro-biological environment and crop yield.AbbreviationsCT No fertilizer addedNPK Inorganic fertilizer onlyM Organic fertilizer only0.5NPKM Organic fertilizer plus inorganic fertilizer (50% of NPK plus 50% of M)0.8NPKM High application ratio of inorganic and organic fertilizers (80% of NPK plus 80% of M) [ABSTRACT FROM AUTHOR]