The lateral transport of labile organic carbon represents a critical pathway for soil organic carbon (SOC) loss, reducing organic carbon sequestration and increasing the risk of waterbody pollution. Livestock manure application on croplands serves as a common fertilizer reduction practice to sustain crop yields, enhance SOC sequestration, and reduce water erosion. However, limited quantitative assessments have examined the effects of livestock manure substitution on labile organic carbon lateral loss and fluxes in long-term experiments. This study conducted a three-year field investigation on subtropical sloping croplands to assess the impact of livestock manure substitution on dissolved organic carbon (DOC) and particulate organic carbon (POC) loss via surface runoff, interflow and eroded sediments. There are four treatments: no fertilization (CK); chemical nitrogen fertilizer (SF), 40% nitrogen substitution with pig manure (PMF), and 100% nitrogen substitution from pig manure (PM). Compared to SF treatment, long-term livestock manure substitution in PMF and PM treatments significantly (P<0.05) reduced annual cumulative surface runoff fluxes by 13.5 and 21.6%, respectively. Manure applications decreased annual sediment fluxes by 12.9 and 19.1%, respectively. Soil water stable aggregates for mean weight diameter (MWD) increased significantly by 37.7 and 73.6%. Annual cumulative POC loss flux via eroded sediment under PMF and PM treatments increased significantly (P<0.05) by 61.1 and 47.9%, respectively. The labile organic carbon loss fluxes, including DOC and POC losses, under PMF and PM treatments increased significantly (P<0.05) by 11.9 and 31.4%, respectively. These results demonstrate that while water erosion intensity decreases due to enhanced soil aggregate stability, the risk of labile organic carbon loss increases after long-term livestock manure substitution in subtropical sloping croplands. Future research should examine labile organic carbon lateral migration under various soil types and slope gradients for livestock manure application in subtropical agricultural ecosystem croplands to better understand extreme rainfall effects.