During TBM tunneling at the great depth, problems such as high in situ stress, groundwater inflow and fractured rock masses are main reasons of the geotechnical risk occurrence in TBM tunneling. Thus it is necessary to modify TBM and optimize TBM operation parameters for improving TBM performance when encountering these adverse geological conditions. In china, two of four headrace tunnels in Jinping II hydropower station project are constructed by two tunnel boring machines. The headrace tunnels are approximately 16.7 km in length and the maximum overburden depth is up to 2,525m. In this paper, the rock masses along the headrace tunnels of Jinping II hydropower station are assessed, and then are classified into three typical excavation sections according to the main controlling factors of TBM excavation. The three typical excavation sections are the normal excavation section, the excavation section controlled by high in situ stress and the excavation section controlled by large groundwater inflow, respectively. In order to overcome the adverse geological conditions in these typical exaction sections, the corresponding modifications and operation optimization for TBM are proposed in this paper. The experiences obtained from Jinping II hydropower station can provide useful reference and guidance for TBM tunneling at depth.