Farm size increase (FSI) accelerates soil erosion and sediment loss into the river. However, it is not clear how large-scale management, including FSI, changes the proportion of sediment from different land use types (LUTs) into rivers in intensive agricultural catchments. Thus, the aim of this study is to quantify and elucidate the contribution of different LUTs to river sediment before and after FSI using compound-specific stable isotopes (CSSI). The study was conducted in three parallel sub-watersheds in the sugarcane plantation region of subtropical southern China, each of which included four different LUTs (eucalyptus plantation, road, sugarcane plantation and channel). Following FSI, the contribution of sediment entering the river from the four LUTs was significantly different from that before FSI. The contribution per unit area of the road, sugarcane, and river channel to river sediment was significantly higher (P < 0.05) after FSI than before FSI. Overall, 1% increase in sugarcane farm size and stream channels caused > 2% and 0.3% increase contribution to river sediment, respectively. Field and road densities significantly correlated with river sediment sources. The FSI had a significant impact on the contribution of sediment entering the river from different LUTs within the watershed. Our results demonstrate that the increase river sediment depends on the increased hydrological connectivity of the watershed due to decreased field density and increased road density. Therefore, it is important to pay attention not only to the agricultural/economic benefits of FSI, but also the negative impacts on increasing erosion and ecological/environmental degradation.