Climate change and biodiversity loss are two of the most serious global environmental challenges faced by humans. As these challenges involve global public goods, it is crucially important that the global society should strive to make synergies between the two most influential United Nations (UN) conventions, which are the UN Framework Convention on Climate Change (UNFCCC) and Convention on Biodiversity. This paper reviews the negotiation process under the two conventions, especially focusing on cross-boundary issues. By analyzing the focal concerns of main parties, this paper evaluates possible future scenarios on cross-boundary issues under the two conventions. For the UNFCCC, focal issues related to biodiversity are as follows: LULUCF (Land Use, Land-Use Change and Forestry); REDD (Reducing Emissions from Deforestation and Forest Degradation); and the international mechanism for Loss and Damage. For the Biodiversity Convention, the major issues related to climate change are: Synergy; REDD; Geo-engineering and related issues. In the end, we propose the following strategies: (1) Integrate the forces of our negotiating team, and promote synergistic actions under two conventions; (2) Plan for negotiations about cross-boundary issues, and take the initiative in the negotiation process; (3) Provide data for risk assessment associated with loss and damage; and (4) Strengthen scientific research and international exchange on geo-engineering issues.