Identifying sediment sources is a prerequisite for developing sediment management strategies. Erosion sediment derived from a small agriculture catchment is an important component of sediment inflow in the Three Gorges Reservoir Area. Paddy fields are one of the major land-use types in this region and can have both positive and negative effects on sediment. In this study, two different source group classification schemes were used to analyze the effect of paddy fields on the sediment in a typical small agriculture catchment in the Three Gorges Reservoir Region. A total of 32 soil source samples were collected from four kinds of land-use types (13 from dry land, 5 from orchards, 8 from paddy fields, and 6 from forest) in the Shipanqiu catchment. Moreover, the properties consisted of 41 elements and 12 element ratios were analyzed. Composite fingerprinting methodology was applied to discriminate and quantify the sediment source contributions. Additionally, element ratio was used as the fingerprint property in the fingerprinting application. The results showed that the element ratio was verified as an effective fingerprint property. Additionally, the relative sediment contributions of the potential land-use sources were 55.25% of dry land, 32.69% of orchards, and 12.06% of forest. Paddy fields played a role of sink rather than of source in this study. Accordingly, both forest and paddy fields are effective sediment management strategies. Particularly, paddy fields are a preferred choice for soil erosion control in mountainous and hilly areas. Furthermore, the proper management of paddy fields can help promote sediment retention and reduce soil erosion, which have positive effects on both the environment and agricultural productivity.