In this work, we performed molecular dynamics simulations to study the dynamics of a shock wave-induced single nanobubble collapsing near one flexible and two rigid boundaries. The flexible boundary consisted of polyethylene, and the rigid boundaries were made of aluminum and iron. The shock waves impinging on the nanobubble inside a molecular system were generated using a momentum mirror approach. For two relative wall distances, we studied the dynamics of the shock-induced single nanobubble and its collapse near the flexible and the rigid boundaries. The atomic velocity contours surrounding the single nanobubble and the collapse-induced damage on the boundaries were analyzed. We obtained this collapse-induced damage from ten collapsing nanobubbles. Results showed that the relative wall distance affected the single nanobubble’s collapse dynamics near the boundaries. A generated nanojet was directed on the surfaces during the collapse process. From the collapse-induced damage point of view, the depth damage of the polyethylene, iron, and aluminum boundaries for the relative wall distance of y = 1.3 were 6.0, 0.47 and 0.63 nm, respectively. It was observed that the extensive collapse-induced damage occurred only on the polyethylene boundary.