Molecular bottlebrushes (MBBs) with a hydrophobic core and a hydrophilic shell may exist as well-defined unimolecular nanoparticles in water. However, they may also aggregate to form large particles if the structure of the hydrophilic and hydrophobic segments fail to be rationally controlled. Herein, a series of core-shell amphiphilic MBBs with a poly (epsilon-caprolactone) (PCL) backbone bearing two block copolymer side chains, poly (butyl acrylate)-b-poly ((oligo (ethylene glycol) acrylate) (PBA-b-POEGA) and poly (butyl acrylate)-b-poly (ethylene glycol) (PBA-b-PEG), were synthesized through grafting-from and grafting-onto strategies. Their hydrophilic shells are different in topology: POEGA is comblike whereas PEG is linear. The stability of the two kinds of MBB with the similar composition as unimolecular nanoparticles in water and their encapsulation capacity for guest-molecule were evaluated. Compared to the MBB with a linear PEG shell, those with comblike POEGA side chains remained stable against aggregation as demonstrated by atomic force microscopy and dynamic light scattering measurement. The MBB with a POEGA shell also displayed a much higher encapsulating capacity to a model guest molecule, pyrene, by hydrophobic interaction. This study provides guidance to the rational preparation of MBBs for applications as molecular vehicles. (C) 2018 Elsevier Ltd. All rights reserved.