Development of the power system towards high renewable penetrated system requires various flexibility resources to grow economically and reliably. However, the multiscale uncertainties brought by the demand and renewable energy sources is increasingly significant in the systems with high proportion of renewable energy. Thus, this paper establishes a system expansion planning model with multiscale uncertainties, in which system elements from all side can develop harmonically, including conventional units, renewable energy sources, transmission lines, energy storage systems and demand responses. The proposed uncertainty architecture consists of a long-term scenario tree which illustrate the uncertain load growth and short-term stochastic scenarios which represent the volatility of wind power, solar power and demand. Simulation operations are then carried out on the planning schemes to evaluate the expected reliability and economics of the resulting systems. The case studies on a 6-bus system and a real-world system in China are conducted to demonstrate the effectiveness of the model. Results show that the flexibility not only comes from coordinated flexibility resources but also the tree structure of planning decisions.