Research projects are primarily collaborative in nature through internal and external partnerships, but what role does funding play in their formation? Here, we examined over 43,000 funded projects in the past three decades, enabling us to characterise changes in the funding landscape and their impacts on the underlying collaboration patterns. We observed rising inequality in the distribution of funding and its effect was most noticeable at the institutional level in which the leading universities diversified their collaborations and increasingly became the knowledge brokers. Furthermore, these universities formed a cohesive core through their close ties, and such reliance appeared to be a key for their research success, with the elites in the core over-attracting resources but in turn rewarding in both research breadth and depth. Our results reveal how collaboration networks undergo previously unknown adaptive organisation in response to external driving forces, which can have far-reaching implications for future policy.