Hollow nanostructures with fascinating properties have inspired numerous interests in broad research fields. Cell-mimicking complex hollow architectures with precise active components distributions are particularly important, while their synthesis remains highly challenging. Herein, a “top-down” chemical surgery strategy is introduced to engrave the 3-aminophenol formaldehyde resin (APF) spheres at nanoscale. Undergoing the cleavage of (Ar)C-N bonds with ethanol as chemical scissors and subsequent repolymerization process, the Solid APF transform to multilevel hollow architecture with precise nanospatial distribution of organic functional groups (e.g., hydroxymethyl and amine). The transformation is tracked by electron microscopy and solid-state nuclear magnetic resonance techniques, the category and dosage of alcohol are pivotal for constructing multilevel hollow structures. Moreover, it is demonstrated the evolution of nanostructures accompanied with unique organic microenvironments is able to accurately confine multiple gold (Au) nanoparticles, leading to the formation of pomegranate-like particles. Through selectively depositing palladium (Pd) nanoparticles onto the outer shell, bimetallic Au@APF@Pd catalysts are formed, which exhibit excellent hydrogenation performance with turnover frequency (TOF) value up to 11257 h–1. This work provides an effective method for precisely manipulating the nanostructure and composition of polymers at nanoscale and sheds light on the design of catalysts with precise spatial active components.