This study examines the modification of thermoplastic starch (TPS) with natural waxes (beeswax, jojoba, and carnauba) in order to tailor the thermal, mechanical, and surface properties of starch-based biocomposites for sustainable packaging applications. TPS was blended with waxes at concentrations from 1 to 50 wt% and processed by compression molding. Thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and dynamic mechanical analysis (DMA) were used to characterize thermal stability, melting transitions, and viscoelastic behavior. Surface wettability was assessed via contact-angle measurements, and morphology was examined using scanning electron microscopy (SEM). The results demonstrate that the type and concentration of wax strongly affect TPS structure and performance. TGA revealed that carnauba slightly increases thermal stability, while jojoba reduces the onset of degradation at higher contents. DSC showed systematic changes in melting endotherms associated with the formation or disruption of wax-rich crystalline phases. DMA indicated that carnauba acts as a reinforcing component, shifting relaxation processes to higher temperatures, whereas jojoba enhances molecular mobility and lowers the α-transition. Beeswax produced intermediate behavior with broadened relaxation profiles. Wettability tests showed that even low additions of beeswax or carnauba markedly increased surface hydrophobicity, whereas jojoba wax resulted in more moderate changes. SEM analysis confirmed a clear morphology–property relationship, showing that moderate wax contents produced a dense and homogeneous TPS structure, while high loadings led to wax-rich phase separation. The study demonstrates that natural waxes serve as effective modifiers of TPS properties, enabling customizable biocomposites suitable for biodegradable and eco-friendly packaging.