The increasing use of nanoscale zero-valent iron (nZVI) for soil and groundwater remediation has raised concerns about its potential effect on soil properties. Numerous laboratory and field studies have demonstrated its excellent capability to immobilize contaminants and enhance contaminated soil. However, a few studies have shed light on the changes in the microstructure and morphology of the soil due to nZVI treatment. This study explores the variation in particle morphology and microstructure in nZVI-treated soil. A series of microscale experiments, including field emission scanning electron microscopy (FESEM), particle size analysis, mercury injection porosimetry (MIP), optical microscopic analysis, and particle shape tests, were conducted on nZVI-treated samples. The dosages of nZVI used were 0%, 0.2%, 1%, 5%, and 10% of the contaminated soil. Morphological characterization suggested that the addition of nZVI resulted in the occurrence of larger-sized particles, on-particle branched structures, finer pore size distribution, aggregation, and a flocculent network in the soil structure. The aggregated and bonded soil particles via nZVI could be one of the mechanisms for its variation in geotechnical characteristics. The findings of this study may improve our understanding of soil improvement using nZVI treatment.