In this study，Chlorella pyrenoidosa GY-D12 was used for large-scale culture to prepare microalgae bio-fertilizer，in order to alleviate a series of environmental problems caused by over-fertilization. Three treatments were set up in the experiment，including microalgae bio-fertilizer(MF)，urea(U)and control(CK). The effects of microalgae bio-fertilizer on soil nutrients，soybean growth and functional genes related to nitrogen transformation were investigated by pot experiment. The results showed that:(1)Compared with CK，MF treatment increased the contents of soil organic matter，total nitrogen，ammonium nitrogen，available phosphorus and available potassium，and reduced the content of soil nitrate nitrogen；(2)Compared with U，MF treatment significantly increased the plant height，root length，root fresh weight，shoot fresh weight，root dry weight and photosynthetic pigment content of soybean，but significantly reduced the number of soybean nodules compared with CK treatment.(3)Compared with CK，MF treatment significantly increased the gene abundance of soil AOA-amoA and AOB-amoA，and accelerated soil nitrification process.(4)Compared with U，MF treatment significantly reduced the soil denitrification functional genes(narG，nirK)abundance，and significantly increased the abundance of nifD and nrfA genes，and promoted the process of soil nitrogen fixation and dissimilatory nitrate reduction to ammonium. Thus，as an organic slow-release fertilizer，microalgal bio-fertilizer can not only support the normal growth of crops，but also effectively reduce nitrogen loss(including leaching，runoff，etc.)and maintain soil nitrogen balance. It is of great significance to realize energy saving，carbon reduction and green development in the process of agricultural production.