Microelectromechanical systems (MEMS) are of considerable interest due to their compact size and low power consumption when used in modern electronics. MEMS devices intrinsically incorporate three-dimensional (3D) microstructures for their intended operations; however, these microstructures are easily broken by mechanical shocks accompanying high-magnitude transient acceleration, inducing device malfunction. Although various structural designs and materials have been proposed to overcome this limit, developing a shock absorber for easy integration into existing MEMS structures that effectively dissipates impact energy remains challenging. Here, a vertically aligned 3D nanocomposite based on ceramic-reinforced carbon nanotube (CNT) arrays is presented for in-plane shock-absorbing and energy dissipation around MEMS devices. This geometrically aligned composite consists of regionally-selective integrated CNT arrays and a subsequent atomically thick alumina layer coating, which serve as structural and reinforcing materials, respectively. The nanocomposite is integrated with the microstructure through a batch-fabrication process and remarkably improves the in-plane shock reliability of a designed movable structure over a wide acceleration range (0–12,000g). In addition, the enhanced shock reliability through the nanocomposite was experimentally verified through comparison with various control devices.