The three-dimension scheduling is defined as the simultaneous application of clock selection and operation scheduling. Previous three-dimension scheduling approach does not consider the interconnect delay. However, with the advent of nanometer era, the interconnect delay may take multiple clock cycles. In this paper, we use convex programming to formulate the three-dimension scheduling problem under multi-cycle interconnect communications. Benchmark data consistently show that our approach achieves the minimum latency within an acceptable run time.