We present a Pareto efficient design method for multi-dimensional optimization of run-time reconfigurable streaming applications on CPU/FPGA platforms, which automatically allocates applications with optimized buffer requirement and software/hardware implementation cost. At the same time, application performance is guaranteed with sustainable throughput during run-time reconfigurations. As the main contribution, we formulate the constraint based application allocation, scheduling, and reconfiguration analysis, and propose a design Pareto-point calculation flow. A public domain solver - Gecode is used in solutions finding. The capability of our method has been exemplified by two cases studies on applications from media and communication domains.