We report on the confined crystallization and polymorphism behavior of a series of comb-like polymers (CS(n)Cs), which were prepared via an N-alkylation reaction between chitosan and n-alkyl bromides (n = 14–20). Analysis by temperature-dependent synchrotron X-ray scattering, Fourier transform infrared spectroscopy (FTIR), solid-state nuclear magnetic resonance spectroscopy (NMR) and differential scanning calorimetry (DSC) revealed that the phase transition and crystalline structure were sensitively controlled by the length scale and the confinement state of alkyl groups, which could induce different packing structures and conformational variation behavior. Remarkably, phase transition from orthorhombic-hexagonal to monoclinic structure was observed for these side-chain polymers, demonstrating that the length scales of alkyl groups and the microstructure of polymeric backbones play an important role in the evolution of packing mode of nano-crystallites.