Self-folding behavior of amphiphilic polymers in aqueous environments mimics the structures of biomacromolecules (e.g., proteins). Since both the three-dimensional structure (static) and the molecular flexibility (dynamic) of a protein are essential for its biological functions, the latter should be considered when designing synthetic polymers that are intended to mimic proteins. Herein, we investigated the correlation between the self-folding behavior of amphiphilic polymers and their molecular flexibility. We synthesized amphiphilic polymers by subjecting N,N-dimethylacrylamide (hydrophilic) and N-benzylacrylamide (hydrophobic) to living radical polymerization. Polymers containing 10, 15, and 20 mol % of N-benzylacrylamide demonstrated self-folding behavior in an aqueous phase. The spin-spin relaxation time (T2) of the hydrophobic segments decreased with the percent collapse of the polymer molecules, indicating that mobility was restricted by the self-folding behavior. Furthermore, comparison of the polymers with random and block sequences revealed that the mobility of hydrophobic segments was not affected by the component of the local segments.