Controlling the hydrophobic behaviors of lignin nanoparticles (LNPs) is crucial and advantageous for their application as film Nano Fillers, yet it poses a significant challenge. Herein, we successfully developed a novel method for the preparation of LNPs with highly hydrophobic behaviors using ternary deep eutectic solution (DES)-H2O systems. The resulting LNPs exhibit a significantly reduced content of hydrophilic groups on their outer surface, leading to a zeta potential value of only −4.9 mV, and up to 140.0° of water contact angle (WCA). Afterwards, a “Dissolution-Restructuration” mechanism was proposed to explain the formation of the prepared LNPs. Firstly, DES demonstrates superior H-bonding capabilities, facilitating the complete disruption of inter- and intramolecular H-bonding in lignin, and resulting in the formation of a highly homogenized lignin network. Subsequently, the DES system undergoes compromise after adding water, triggering the reformation of both inter- and intramolecular H-bonding and π-π interactions. Consequently, lignin orderly self-assembles into LNPs with highly hydrophobic characteristics. Especially, using the as-prepared LNPs as Nano fillers, a series of LNPs-containing polyvinyl alcohol (PVA) films were successfully fabricated, exhibiting exceptional hydrophobic behaviors (with contact angles reaching up to 124.0°). Furthermore, the mechanical strength, UV-shielding capabilities, and biodegradability of the PVA films are significantly enhanced. This study introduces a sustainable and efficient approach for the synthesis of hydrophobic LNPs, thereby facilitating the broadening of applications for lignin-based functional composite film materials.