Nano-satellite is a kind of advanced and effective tool for space exploration. And the nano-satellite formation flight technology becomes more and more important in distributed space exploration. Thus a design of high performance management and control system (named MCS) of nano-satellite for formation space exploration is presented in this paper. Different with traditional design concept for satellites, MCS adopts a modular configuration not only to satisfy composite requirements of processing capacity, integration, cost and power of nano-satellite, but also to fit applications in formation flight experimentation. MCS includes OBC (on-board computer) module, attitude & orbit control module, telemetry & telecommand module, and power management module. Furthermore, as core component the design uses reconfiguration scheme and COTS (commercial-off-the-shelf) technology, so it shows an outstanding performance in high efficiency, high reliability, low power and low cost for satellite engineering applications.