Abstract: Biodiversity is not only important strategic resource, but also the safeguard to the ecological security and success of the development of ecological civilization. Gathering "big data" of biological sciences at different levels, the in-depth data mining and novel discoveries stemmed from cross disciplines will switch life sciences to the new data-intensive science paradigm, and eventually leads to the change of the way how life system should be understood, and how biodiversity resources should be utilized sustainably. Therefore, to establish an infrastructure for the big biodiversity data in China is urgently needed. This infrastructure incorporates big biodiversity data from both macro and micro scales, and integrates data services and data mining system. It incorporates in-depth data mining tools, simulation models, standards for compiling and sharing data of biodiversity and ecosystems. In this system, the big data from palaeontology and genomics, diversity of species and ecosystems are well integrated. The datasets from geography, climatology, remote sensing, environmental and social sciences, and economics are also included as a comprehensive visualized big data platform being available to the public. It could be used to promote sound decision making for biodiversity conservation and ecological security in China. These services will also contribute greatly to the advancement of biodiversity science, the industrial innovation and development, providing fundamental information for fulfilling the national obligations in implementing the Convention on Biological Diversity, the prevention and control of invasive alien species and the monitoring of international trade of wildlife, and so on.