A facility secondary NO3− salinized soil modifier and a modification method are disclosed. The present invention involves the preparation processes of two biological soil modifiers A and B and application methods thereof, which are specifically described as follows: (1) soil modifier A: solid, obtained by microbial fermentation with straw powder and rice bran and the like as raw materials, C/N between 30-50, applied by uniformly mixing at 1-1.4‰ by mass with facility ploughing soil, co-culturing at 35-50° C. for 5-7 days, and then returning to fields; and (2) soil modifier B: liquid, subjected to salt tolerance acclimation to have effective microbial populations, and used in the crop growth period. Based on the microbial techniques, the present invention can improve soil structureness, enhance microbial activity and promote biological immobilization on inorganic nitrogen in soils, significantly increasing the facility cultivation crop yield, and improving the product quality.