In this study, we examined the self-assembly of a series of biodegradable and biocompatible amino acid-based polyhydroxyurethanes (PHUs), investigating the structural influence of these polymers on their self-assembly and the resulting morphological features. The presence of hydrophilic and hydrophobic segments, along with carbonyl urethane, ester, and hydroxyl groups in the PHU backbone, facilitates intermolecular hydrogen bonding, enabling the formation of self-assemblies with hierarchical nanodimensional morphologies. We determined the critical aggregation concentration (CAC) and found that it largely depends on the PHU's structure. In-depth morphological studies demonstrated that the evolution of morphology proceeds in four steps: (1) the initial formation of micelles, which act as seeds at very low concentrations, (2) the elongation of these micelles into nanorod or nanopalette shapes below the CAC range, (3) the epitaxial growth of nanofibers at the CAC, and (4) the complete formation of fibrous mats above the CAC. Additionally, these hierarchical structures were utilized for the encapsulation and release of the drug doxorubicin (DOX). We observed that 75% of the encapsulated DOX was readily released in a mildly acidic environment, similar to the physiological conditions of cancer cells. Cellular uptake studies confirmed the effective uptake of the drug-loaded nanoassemblies into the cytoplasm of cells. Our studies also confirmed that these self-assembled structures can serve as effective cell adhesive scaffolds for tissue engineering applications.