Nowadays, most research results on ecosystem services in Karst areas are limited to a single function of an ecosystem service. Few scholars conduct a comparative study on the mutual relationships among ecosystem services, let alone reveal the trade-off and synergic relationships in typical Karst watershed. This research aims to understand and quantitatively evaluate the relationships among ecosystem services in a typical Karst watershed, broaden the depth and width of trade-off and synergic relationships in ecosystem services and explore a set of technical processes involved in these relationships. With the Shibantang Karst watershed in China as the research site, we explore the trade-off and synergic relationships of net primary productivity (NPP), water yield, and sediment yield by coupling Soil and Water Assessment Tool (SWAT) and Carnegie-Ames-Stanford Approach (CASA), and simulating and evaluating these three ecosystem services between 2000 and 2010. Results of this study are as follows. (1) The annual average water yield decreased from 528 mm in 2000 to 513 mm in 2010, decreasing by 2.84%. (2) The annual average sediment yield decreased from 26.15 t/ha in 2000 to 23.81 t/ha in 2010, with an average annual reduction of 0.23 t/ha. (3) The annual average NPP increased from 739.38 g Cm-2 a(-1) in 2000 to 746.25 g Cm-2 a(-1) in 2010, increasing by 6.87 g Cm-2 a(-1). (4) Water yield and sediment yield are in a synergic relationship. The increase of water yield can accumulate the soil erosion amount. NPP is in a trade-off relationship with water yield and sediment yield. The improvement of NPP is good for decreasing water yield and soil erosion amount and increasing soil conservation amount. This study provides policy makers and planners an approach to develop an integrated model, as well as design mapping and monitoring protocols for land use change and ecosystem service assessments.