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New energy power supply system (NEPSS) is a promising development trend of small and medium-sized island power system. NEPSS has three major characteristics. First, there is a high proportion of new energy generation (NEG) in the NEPSS. Second, NEPSS is exposed to more natural disasters. Third, autonomous operation is widely adopted in the NEPSS. In this paper, energy management system architecture is designed for NEPSS. In the architecture, there are seven modules: bad data identification and repair module, state estimation and pattern recognition module, load and NEG forecasting module, security early warning and protecting module, dispatch plan module, disaster assessment and disposal module, and black-start decision support module. The NEPSS dispatch plan is specifically discussed in term of different horizons and operation modes. Finally, a rolling method for adjustments of dispatch plans is proposed.