Networking of microgrids has received increasing attentions in recent years, which requires the uncertainty management associated with variations in the system. In this paper, a two-stage energy management strategy is developed for networked microgrids under the presence of high renewable resources. It decomposes the microgrids energy management into two stages to counteract the intra-day stochastic variations of renewable energy resources, electricity load and electricity prices. In the first stage (hourly time scale), a hierarchical hybrid control method is employed for networked microgrids, aiming to minimize the system operation cost. The mean variance Markowitz theory is employed to assess the risk of operation cost variability due to the presence of uncertainties. In the second stage (5-min time scale), the components in microgrids are optimally adjusted to minimize the imbalance cost between day-ahead and real-time markets. Simulation study is conducted on an uncoordinated microgrids system as well as on the proposed networked system. According to the simulation results, the proposed method can identify optimal scheduling results, reduce operation costs of risk-aversion, and mitigate the impact of uncertainties.