The presence of abundant hydrophilic hydroxyl groups on the surface of paper fibers limits their application in barrier packaging. Currently, petroleum-based materials commonly used to enhance the barrier performance of paper are often non-biodegradable. In contrast, alkali lignin offers unique advantages for the preparation of barrier packaging materials due to its inherent biodegradability, hydrophobicity, and flame-retardant properties. To investigate the influence of alkali lignin on the hydrophobic performance of packaging paper, this study used alkali lignin (A-Lig) as a raw material and modified it via esterification with palmitoyl chloride and stearoyl chloride, synthesizing lignin palmitate (Lig-P) and lignin stearate (Lig-S). Subsequently, coating solutions were formulated based on A-Lig, Lig-P, and Lig-S, and applied to base paper using a cross-spraying method to fabricate a series of lignin-coated papers. The chemical structures, micro-morphologies, and thermal properties of A-Lig, Lig-P, and Lig-S were systematically characterized using Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), nuclear magnetic resonance (NMR), scanning electron microscopy (SEM), and thermogravimetric analysis (TGA). The microstructure, hydrophobic properties, and mechanical strength of the base paper and coated papers were evaluated through measurement of static water contact angle, rolling angle, water absorption, water stability on the paper surface, self-cleaning performance, and mechanical properties. The results show that the hydroxyl groups in lignin are effectively substituted after esterification modification, with successful grafting of aliphatic chains. The relative content of C—O bonds decreases, and the thermal stability is slightly reduced. The static water contact angles of the base paper (Bas-P), A-Lig-coated paper (Lig-P1), Lig-P-coated paper (Lig-P2), and Lig-S-coated paper (Lig-P3) are 45.9°, 83.5°, 150.8°, and 151.6°, respectively. Meanwhile, the rolling angles of Lig-P2 and Lig-P3 are 9.3° and 3.5°, achieving a superhydrophobic effect. The micro-surfaces of both Lig-P2 and Lig-P3 exhibit a petal-like micro-nano rough structure, significantly reduced water absorption, and demonstrate excellent water stability and self-cleaning performance. Compared to Bas-P, Lig-P2 and Lig-P3 exhibit a slight decrease in tensile strength but a pronounced increase in elongation at break, indicating improved flexibility of the paper.