Abstract: Nowadays the human living environment faces grave challenges raised by a series of environmental issues, including water pollution and the greenhouse effect. These crises call for the development of novel materials with functional properties for effective environmental engineering control and robust mechanics to manage various complex conditions. Herein, taking inspiration from dandelion blowballs, we propose a fabrication strategy to prepare hierarchically structured chitosan aerogel beads by combining droplet freeze casting and silylation grafting. The chitosan aerogel beads consist of a hierarchical structure, with a spherical macro-shape, a centrosymmetric radially aligned microstructure, and a nano-scale siloxane coating. As a result, the dandelion-like hierarchical structure endows the aerogel beads with a fine combination of high mechanical efficiency and functional properties. With an average density of only 0.08 g/cm3, the aerogel beads can sustain more than 2.2 MPa of stress at 80% deformation. Their chitosan skeleton, despite being inherently water dissolvable, is modified to be highly hydrophobic (contact angle = 147°, rolling angle = 4.2°), even under prolonged water blasts. Further, the aerogel beads not only showcase the capability to quickly absorb various pollutants with good reusability, but also can be assembled into customizable configurations, demonstrating their filtration capability and excellent thermal insulation with a thermal conductivity of 32.5 mW·m−1·K−1. Benefiting from these excellent properties, our aerogel beads represent a promising engineering material for water treatment and thermal insulation. Also, this work demonstrates a novel approach that couples both material and structural designs for architectured aerogels with excellent mechanical and functional properties.