Land-based microplastics (MPs) are considered the primary source of MPs in aquatic environments, with runoff being a major pathway for their transfer from soil to surface water. However, the transportation characteristics of MPs via agricultural surface runoff remain unclear. In this study, we investigated the occurrence and emission characteristics of MPs in agricultural surface runoff under various short-term fertilizer applications and natural rainfall events using laser direct infrared imaging analysis (LDIR). MPs from fertilizers and soils co-migrated with the agricultural runoff. The abundance and concentration of MPs in runoff were 145.90 ± 22.48–2043.38 ± 89.51 items·L−1 and 39.17 ± 21.94–523.04 ± 47.85 µg·L−1, respectively. Small and low-density MPs, such as polyethylene (PE), chlorinated polyethylene (CPE), and polyurethane (PU) in film/fragment form with 20–50 µm exhibited a higher mobility. No statistical differences were observed in the distribution of runoff MPs with the application of different fertilizers. There was a significant positive relationship between runoff MP abundance and rainfall intensity. The annual emission load in this study area was 116.73 g·hm−2, indicating that the transportation of MPs via agricultural surface runoff cannot be ignored. This study is conducive to understanding the migration behavior of MPs in soil-water environments in a better manner.