Abstract Black phosphorus (BP) is emerging as a rising star in the post graphene nanomaterials, manifesting intriguing thickness‐dependent properties. However, there is little knowledge about the structural and mechanical stabilities of such BPs and their thickness dependence. Using high pressure technique, a comprehensive study was performed on the thickness‐dependent structural variations of BPs. It has been revealed from high pressure phase diagram that decrease of thickness enhances the structure stability of BPs, which is prominent between 71 and 13 nm. More importantly, an inhomogeneous distortion of the lamellar puckered structure is observed on these BPs, and the thinner ones exhibit enhanced anisotropic compressibility, with a rigid interlayer and zigzag structure and a relatively flexible armchair structure. This systematic study not only provides insights into thickness‐dependent structural nature of BPs but also lays foundation toward design and fabrication of BP‐based devices.