Fusarium crown and root rot is among the world's major agricultural diseases caused by Fusarium. oxysporum f. sp. radicis-lycopersici, which always resulted in serious damage to vegetable production worldwide. Pyraclostrobin is a broad-spectrum and highly effective fungicide with strong activity against F. oxysporum f. sp. radicis-lycopersici. However, the limited distribution of pyraclostrobin in the soil compromises its field fungicidal performance due to the difficulty in providing a large protection zone surrounding the growing root system of the plant. Nanotechnology offers a great opportunity to develop new strategies for functionalized pesticide loading systems. In this study, the physicochemical properties of pyraclostrobin in the soil were manipulated by encapsulating the active ingredients in a lignin-modified polymer nanocapsule (NCS) to produce a nanoscale delivery system with excellent soil mobility. These nanocapsules exhibited a stable core-shell structure and rapid release performance. In addition, they also increased the distribution of particles on the surface of target organisms and enhanced the soil mobility of pyraclostrobin, mainly benefitting from the nanocapsule's negatively charged polymer shell and nanoscale size. Pot experiments showed that, compared to treatment with nanosized emulsion in water (NEW) and micron-grade microcapsule suspension (CS) of pyraclostrobin, the NCS provided improved control efficacy on tomato crown and root rot. They also showed lower pesticide residue in the soil than CS treatment.