In this paper, the bubble dynamics and the mechanism of dry spot formation during boiling on a two-level hierarchical structured surface are numerically investigated using a three-dimensional thermal multiphase lattice Boltzmann model with liquid–vapor phase change. The hierarchical structured surface consists of three parts: a smooth surface basement, primary pillars on the basement, and secondary pillars overlaid on the primary pillars. It is found that the boiling heat transfer on the hierarchical structured surface is significantly dependent on the bubble departure frequency and the dry area fraction, which are in turn affected by the structural parameters of secondary pillars. Increasing the height or width of the secondary pillars is found to effectively increase the bubble departure frequency, but it may also enlarge the size of dry spots on the hierarchical structured surface. The numerical investigation shows that, in order to prevent the formation of dry spots on the hierarchical structured surface, an effective approach is to reduce the proportion of the contact line on the lateral walls of secondary pillars to the whole contact line, which can be realized by reducing the area of the lateral walls of secondary pillars or appropriately increasing the secondary pillar spacing. The optimum boiling performance on the hierarchical structured surface is found to be achieved under the situation that the bubble departure frequency is sufficiently high, but the dry spot area is as small as possible.