Keeping the soil layer moist and incorporating with fertilization can effectively improve soil structure and improve soil microbial activity. This article explored the interaction mechanism between fertilization and precipitation on the root, seedling, soil and microbe of raw soil cotton. And the results can provide a scientific basis for rational fertilization of raw soil cotton under different precipitation years. The experiments were conducted out for 3 consecutive years and the test soil was loess parent raw soil. The experiments explored the effects of nitrogen(N), phosphorus(P), NPK compound fertilizer(NPK)and organic fertilizer(ORG)on raw soil ripening, when the fertilization depth was 0~20 cm. The experiments also surveyed the impacts of ORG, ORG+NPK on raw soil ripening under drought, flat water and abundant water as three types of precipitation, when the fertilization depth was 40~60 cm. The results showed that the ORG under 0~20 cm significantly increased cotton pole weight, total weight of cotton peach and total aboveground biomass. The ORG or P significantly improved soil nutrition of raw soil cotton rhizosphere, root nutrition and enzyme activities. The ORG significantly enhanced the soil microbial diversity and abundance. Under the same fertilization measure, precipitation played an important role on soil ripening. The ORG under drought and flat water significantly enhanced cotton yield. ORG and NPK under flat water, ORG under drought or abundant water could effectively improve soil microbial diversity. The comprehensive analysis showed that fertilization measure for rapid improving and ripening soil of raw land was ORG+P. Regarding to the precipitation, ORG+NPK under flat water, ORG under drought and abundant water were the best fertilization types to speed up raw soil ripening and improve soil microbial diversity.