Realizing clean energy supply is important for the sustainable development of pelagic island. The volatility and randomness features of renewable energy generation may reduce power supply reliability, thus backup units is necessary in micro-grid in pelagic island. This paper proposed a dual-standby configuration scheme based on Sequence Operation Theory to achieve reliable power standby. Firstly, characteristics of standby units, micro gas turbine and diesel generator, are analyzed. Next, the probability distribution function models of wind, photovoltaic and load demand in pelagic island are established, and the reliability index of power shortage probability is calculated by Sequence Operation Theory. Then, the two-stage dual-standby control scheme to make full use of the complementary standby units is introduced and object function to minimize equivalent annual cost on the premise of satisfying probabilistic reliability index is modeled. Hybrid integer particle swarm algorithm is used to solve the problem. Finally, the proposed model for dual-standby configuration is applied to a pelagic island. The simulation results show that the proposed method can meet the load demand in both daily and extreme weather and achieve superior economy.