Atopic dermatitis (AD), a prevalent skin condition often complicated by microbial infection, poses a significant challenge in identifying the responsible pathogen for its effective management. However, a reliable, safe tool for pinpointing the source of these infections remains elusive. In this study, we propose a novel on-site pathogen detection that combines chemically functionalized nanotopology with genetic analysis to capture and analyze pathogens closely associated with severe atopic dermatitis. The chemically functionalized nanotopology features a 3D hierarchical nanopillar array (HNA) with a functional polymer coating, tailored to isolate target pathogens from infected skin. This innovative nanotopology demonstrates superior pathogenic capture efficiency, favorable entrapment patterns, and non-cytotoxicity. We utilize an HNA-assembled stick to directly retrieve bacteria from infected skin samples, followed by extraction-free quantitative loop-mediated isothermal amplification (direct qLAMP) for validation. To mimic human skin conditions, we employ porcine skin, successfully capturing Staphylococcus aureus, a common bacterium exacerbating AD cases. Our on-site detection method exhibits an impressive detection limit of 10^3 cells/mL. The HNA-assembled stick represents a promising tool for on-site detection of bacteria associated with atopic dermatitis. This innovative approach enables to deepen our understanding of AD pathogenesis and open avenues for more effective management strategies for chronic skin condition. This article is protected by copyright. All rights reserved.