In a small watershed with a typical agro-forest complex ecosystem and peak-cluster valley landform of the central Guizhou,¹³⁷Cs and magnetic susceptibility were used as compound fingerprinting factors to analyze the fingerprint characteristics of carbonate rock surface soil (from hill slopes and depressions), deep soil (from river bank or fissures and grikes), and clastic rock pieces. A multivariate mixing model was used to trace the probable sources of suspended sediment in discharge generated during rainstorm events, and calculate the main source and the relative contribution of the sediment from surface and underground outlets of small watershed. The results showed that the concentration of ¹³⁷Cs and magnetic susceptibility were significantly different in the three types of sources. The average ¹³⁷Cs and magnetic susceptibility values of surface soil, deep soil and clastic rock pieces were 3.39 Bq/kg and 310.07×10^-8 m³/kg, 0.50 Bq/kg and 180.69×10^-8 m³/kg, 0 Bq/kg and 7.90×10^-8 m³/kg, respectively. The relative contributions of surface soil, deep soil and clastic rock pieces to the sediments of the surface outlet were 16.2%, 4.3% and 79.5%, respectively, and the goodness of model fit was 99.97%. The relative contributions of surface soil, deep soil and clastic rock pieces to the sediments of the underground outlet were less than 0.1%, 37.9% and 62.1%, respectively, and the goodness of model fit was 83.80%. The sediment sources in this karst watershed differed from those in typical non-karst terrain, the specific characteristics were:(1) The sediment from carbonate surface soil was few, and carbonate surface soil contributed mainly to the surface water system, while contributed little to river sediment; (2) Clastic rock pieces were the primary source of both surface and underground river sediments; (3) Deep soil contributed slightly, and it contributed more to underground rivers than to surface rivers. In addition,¹³⁷Cs and magnetic susceptibility could be used as compound fingerprinting tracers to trace the sediment source of the surface and subsurface rivers in this karst area, and also could be applied to determine the relative contribution rate of sediment sources.