There is a growing need for both science and practice domains to collaboratively and systematically seek knowledge-based strategies for sustainable development. In recent years, transdisciplinary research has emerged as a new approach that enables joint problem solving among scientists and stakeholders in various fields. In this paper, we aim to introduce transdisciplinary research for supporting the integration of the concept of ecosystem services into land and water management in the Tarim River Basin, Xinjiang, Northwest China. While a large number of ecosystem service studies have helped to raise the awareness for the value of nature in China, a number of challenges remain, including an improved understanding of the relationships between ecosystem structure, functions and services, and the interaction of the various ecosystem services. A meaningful valuation of ecosystem services also requires the consideration of their strong spatial heterogeneity. In addition, ways to introduce the concept of ecosystem services into decision-making in China need to be explored. Thus, successful integration of the concept of ecosystem services into actual land and water management requires a broad knowledge base that only a number of scientific disciplines and stakeholders can provide jointly, via a transdisciplinary research process. We regard transdisciplinary research as a recursive process to support adaptive management that includes joint knowledge generation and integration among scientists and stakeholders. System, target, and transformation knowledge are generated and integrated during the process of (1) problem (re)definition, (2) problem analysis and strategy development, and (3) evaluation of the impact of the derived strategy. Methods to support transdisciplinary research comprise participatory modelling (actor-based modelling and Bayesian Networks modelling) and participatory scenario development. Actor-based modelling is a semi-quantitative method that is based on the analysis of problem perspectives of individual stakeholders as depicted in perception graphs. With Bayesian Networks, complex problem fields are modelled probabilistically in a simplified manner, using both quantitative data and qualitative expert judgments. These participatory methods serve to integrate diverse scientific and stakeholder knowledge and to support the generation of actually implementable management strategies for sustainable development. For the purpose of integrating ecosystem services in land and water management in the Tarim River Basin through transdisciplinary research, collaboration among scientists and institutional stakeholders from different sectors including water, agriculture, forestry, and nature conservation is required. The challenge is to adapt methods of transdisciplinary research to socio-cultural conditions in China, particularly regarding ways of communication and decision-making.