In multi-FPGA systems, time-division multiplexing (TDM) is a widely used technique to transfer signals between FPGAs. While TDM can greatly increase logic utilization, the inter-FPGA delay will also become longer. A good time-multiplexing scheme for inter-FPGA signals is very important for optimizing the system performance. In this work, we propose a fast algorithm to generate high quality time-multiplexed routing results for multiple FPGA systems. A hybrid routing algorithm is proposed to route the nets between FPGAs, by maze routing and by a fast minimum terminal spanning tree method. After obtaining a routing topology, a two-step method is applied to perform TDM assignment to optimize timing, which includes an initial assignment and a competitive-based refinement. Experiments show that our system-level routing and TDM assignment algorithm can outperform both the top winner of the ICCAD 2019 Contest and the state-of-the-art methods. Moreover, compared to the state-of-the-art works [17], [22], our approach has better run time by more than 2X with better or comparable TDM performance.