Fallowing is regarded as an effective method for the self-recovery management of farmland and is generally used in cultivated land management. Studies have shown that long-term fallow has many ecological and environmental benefits. However, the long-term fallowing of farmland has also caused a decline in the grain production of farmland for a period of time. Short-term fallow can reduce the risk of food insecurity, but there are few studies on short-term fallow, especially on the comparation of different fallowing management methods and their relationship with soil microbial ecology. Our study has focused on seven treatments. Firstly, the traditional farming method was set as the control group. Native vegetation and crop-pasture vegetation were set as the fallowing vegetation. There were three irrigation–fertilization levels for each vegetation. The effects of the sampling times showed that the impact of fallow management on the soil properties became gradually stronger with time. The interactions between the sampling times and treatments showed a significant impact on organic carbon and total nitrogen. There was a significant impact of fallow management on the inorganic carbon accumulation and ammonia nitrogen consumption. Microbial biomass carbon was significantly increased by fallowing. Fallowing with irrigation could enhance the soil microbial nitrogen transformation. Some genera associated with assisting diseases were significantly increased by the native vegetation fallow and grass fallow with farmyard manure. The fallow with native vegetation showed more advantageous ecological benefits than the crop-pasture vegetation fallow. Although the crop-pasture vegetation followed the principle of ecological intensification, it failed to show better ecological benefits in the short fallow period. In irrigation management, the benefits of native vegetation and crop-pasture vegetation are similar. However, considering the lower cost of crop-pasture vegetation, crop-pasture vegetation fallow with irrigation could be a better choice. If it is difficult to implement conservation measures during the fallowing process, native vegetation fallowing without management may be the only fallowing choice.

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