Multiple field programmable gate array (Multi-FPGA) systems are capable of forming larger and more powerful computing units through high-speed interconnections between chips and are beginning to be widely used by various computing service providers. However, the new computing architecture brings new challenges to the system’s task resource management. Existing resource management methods do not fully exploit resources in Multi-FPGA systems, and it is difficult to support fast resource request and release. In this regard, we propose a geometric layout-based resource management (GLRM) method for Multi-FPGA systems. First, a geometric layout-based task combination algorithm (TCA) was proposed to ensure that the final system can use the available FPGA resources more efficiently. Then, we optimised two resource management algorithms using TCA. Compared with state-of-the-art resource management methods, TCA increases resource flexibility by an average of 6% and resource utilisation by an average of 7%, and the two optimised resource management methods are effective in improving resource management performance.