The spatially precise integration of arrays of micropatterned two-dimensional (2D) crystals onto three-dimensionally structured Si/SiO2 substrates represents an attractive, low-cost system-on-chip strategy toward the realization of extended functions in silicon microelectronics. However, the reliable integration of such atomically thin arrays on planar patterned surfaces has proven challenging due to their poor adhesion to underlying substrates, as ruled by weak van der Waals interactions. Here, we report on an integration method utilizing the flexibility of the atomically thin crystals and their physical subsidence in liquids, which enables the reliable fabrication of the micropatterned 2D materials/Si arrays. Our photodiode devices display peak sensitivity as high as 0.35 A/W and external quantum efficiency (EQE) of ∼90%. The nano-subsidence technique represents a viable path to on-chip integration of 2D crystals onto silicon for advanced microelectronics.