Compared to traditional biochar (BC), nano-biochar (NBC) boasts superior physicochemical properties, promising extensive applications in agriculture, ecological environments, and beyond. Due to its strong adsorption and migration properties, NBC may carry nutrients or pollutants to deeper soil layers or even groundwater, causing serious environmental risks. Nevertheless, the migration rules and mechanisms of NBC in soil are still unclear. Therefore, this study employed soil column migration experiments to systematically explore the migration rules and mechanisms of NBC under various flow rates, initial soil water contents, soil depths, and soil textures. The results showed that regulated by smaller particle size differences and greater surface charges, NBC exhibited a stronger migration ability compared with traditional BC. As the soil texture transitioned from fine to coarse, the migration capability of NBC significantly improved, driven by both pore structure and interaction forces as described by the DLVO theory. The migration ability of NBC was also greatly boosted as the soil transitioned from saturated to unsaturated conditions, primarily because of preferential flow. When the flow rate increased from 70% KS to 100% KS and 130% KS, the migration ability of NBC also increased accordingly, as changes in injection flow rates altered the velocity distribution of pore water. NBC in 25 cm soil columns was more prone to shallow retention compared with 10 cm soil columns, resulting in weaker overall migration ability. In addition, through fitting of the two-site kinetic model and related parameters, the penetration curves of NBC under various variable conditions were effectively characterized. These findings could offer valuable insights for NBC’s future efficient, rational, and sustainable utilization, facilitating the evaluation and mitigation of its potential environmental risks.