Modern embedded devices require high performances such as computing, throughput and power consumption. Multiprocessor System-on-Chip (MPSoC) is a promising solution to meet the requirements. And the Network-on-Chip (NoC) is used as the interconnection of MPSoC. Whereas it brings more challenge on application programming and fast design exploration of software and hardware implements automatically. In this paper we propose a cluster MPSoC architecture, which adopts hybrid interconnection of processor clusters and NoC. And we present a design automation and synthesis methodology to generate MPSoCs in a system-level way for multiple application use-cases. And it merges them onto a minimal hardware architecture of resources. The desired MPSoC design is generated with short design time, making it suited for fast design exploration for MPSoC development. The proposed design flow is implemented into a tool for Xilinx FPGAs. The experiments results illuminate that our design methodology is a convenient approach to generate the MPSoC design for multiple use-cases.