Since natural cellulose is mostly cellulose I and has a fibrous form, most cellulose-based adsorbents are fibrous/rod-shaped and exhibit the cellulose I crystal structure. This study reports a cellulose II-based spherical nanoparticle microcluster adsorbent (SNMA), synthesized from biomass by a bottom-up approach, for removing toxic hexavalent chromium (Cr(VI)). The basic structure of SNMA was investigated. Notably, the prepared adsorbent was a microcluster composed of spherical nanoparticles, while exhibiting cellulose II crystal structure, resulting in higher thermal stability and significantly enhanced adsorption performance. The adsorption process and mechanism of SNMA on Cr(VI) were studied in detail. The SNMA achieved a high adsorption capacity (225.94 mg/g) and receptor site density. The SNMA is expected to be used as a bio-based spherical nanoparticle microcluster adsorbent platform for the adsorption of different toxic substances by changing the surface functional groups of its components, spherical nanoparticles.