Increasing the share of renewable energy in total power generation is an important trend in the global power system. However, the volatility and intermittency of renewable energy resources pose a great challenge to the high penetration of renewable energy. In order to absorb large amount of renewable energy electricity, thermal power plants should increase their operational flexibility such as more start-up and shut-down actions as well as running at part load more often. It brings about integration costs for renewable energy penetration, which should be quantitatively assessed. In this paper, a long-term power generation expansion planning model incorporating short-term operational characteristics of power generation units is proposed. This model is used to find the most cost effective low carbon transition pathway of power sector with high penetration of renewable energy and the impact of incorporating short-term integration costs on long-term power generation planning. China is selected for a case study as it is the largest carbon dioxide emitter in the world and has urgent need for low carbon transition.