Transdisciplinary research increases to produce scientifically robust and socially relevant solutions for complex sustainability issues, through knowledge integration and mutual learning between scientists and praxis stakeholders, which became the mainstream of sustainability science. The key issues in transdisciplinarity are science-practice interaction, stakeholder participation, and knowledge integration. To address these issues, this article first review the current trend of transdisciplinary theories and methodologies, then take Chinese-German cooperated project on sustainable land management in Southwest China as a case study to reflect on the key management issues of transdisciplinary research, and discuss the elements and principles for successful transdisciplinary research. It is pointed out that scientists and practitioners need to change their perspective from the traditional science-driven research paradigm, raise awareness of the importance of communication and participation in knowledge generation, and improve their communication skills to better interact with each other. Project managers need to create suitable means so that stakeholders participate in and contribute to the solution development actively, and have ownership of the process and the solution. Understanding and accepting heterogeneity among stakeholders is a precondition for collaboration and negotiation. Power relations need to be carefully addressed so that all stakeholders and their opinions are equally valued. Translation and the role of the translator should be considered in for better communication across cultural and professional boundaries. For process management, iteration, reflexivity, dynamic and flexibility are important principles to timely adapt to specific or unexpected situations. Specific design and adjustment are needed concerning the cultural context of each specific case.