Abstract: The environmental risk caused by successive and heavy application of mineral fertilizer has attracted wide attention, but scarce for that of compost.After fully investigation of the local fertilization rate of mineral fertilizer in winter wheat-rice cropping system, the dose of compost applied was determined according to the amount of total nitrogen contained in mineral fertilizers, and a 3-year (a total of six seasons) field experiment was carried out to study the environmental risk derived from compost heavy application. Soil samples were analyzed after the third year of rice harvested of the plough layer soil(0-25 cm). It was found that mineral fertilizer and compost may both result in environmental risk after the 3-year successive and heavy application. In contrast to the untreated control (CK), heavy application of mineral fertilizer (CF) easily lead to soil acidification and nitrate accumulation, while soil phosphorus and heavy metals (Zn, Cu, CD and Ni) content increased significantly when manure-based compost carried the same amount of total nitrogen with mineral fertilizer was applied (CP); In addition, heavy application of mineral fertilizer and compost both caused significant decrease of SMBN/TN ratio, SMBC/SOC ratio and bacterial diversity. The results of this study may be conducive to the rational application of compost in the future.