Nitrogen fertilizer unabsorbed by crops eventually discharges into the environment through runoff, leaching and volatilization, resulting in three-dimensional (3D) pollution spanning from underground into space. Here we describe an approach for controlling nitrogen loss, developed using loss control fertilizer (LCF) prepared by adding modified natural nanoclay (attapulgite) to traditional fertilizer. In the aqueous phase, LCF self-assembles to form 3D micro/nano networks via hydrogen bonds and other weak interactions, obtaining a higher nitrogen spatial scale so that it is retained by a soil filtering layer. Thus nitrogen loss is reduced and sufficient nutrition for crops is supplied, while the pollution risk of the fertilizer is substantially lowered. As such, self-fabrication of nano-material was used to manipulate the nitrogen spatial scale, which provides a novel and promising approach for the research and control of the migration of other micro-scaled pollutants in environmental medium.