In this paper, we first propose an HDR-mcd architecture, which integrates periodically all-in-phase based multiple clock domains and multi-cycle interconnect communication into high-level synthesis. In HDR-mcd, an entire chip is divided into several huddles. Huddles can realize synchronization between different clock domains in which interconnection delay should be considered during high-level synthesis. Next, we propose a high-level synthesis algorithm for HDR-mcd, which can reduce energy consumption by optimizing configuration and placement of huddles. Experimental results show that the proposed method achieves 32.5% energy-saving compared with the existing single clock domain based methods.