High usage and low efficiency of fertilizers not only restrict sugarcane production but also destroy the soil environment in China. To solve this problem, a network-structured nanocomposite as a fertilizer synergist (FS) was prepared based on attapulgite (ATP) and polyglutamic acid (PGA). Field demonstrations were conducted from 2020 to 2021. Leaching tests and characterization were used to evaluate the ability of the network structure to control nutrient loss. The effects of FS on sugarcane growth and field soil quality were also investigated. The results showed FS could effectively reduce nitrogen loss by 20.30% and decrease fertilizer usage by at least 20%. Compared to fertilizer with the same nutrition, fertilizer with FS could enhance sugarcane yield and brix by 20.79% and 0.58 percentage points, respectively. Additionally, FS improved the soil physicochemical properties, including reducing the soil bulk density and increasing the contents of nitrogen, phosphorus, potassium, and organic matter. FS also altered the diversity of the bacteria and improved the bacterial richness. Our study shows this FS has a good ability to control nutrient loss, advance sugarcane agronomic traits, and improve soil quality. This work offers an option for the sustainable development of sugarcane through the novel FS.