The high hydrophilicity and brittleness of cellulose acetate (CA) limit its application as a barrier and as a moistureproofing, waterproofing, and self-cleaning agent. Imparting CA films with hydrophobicity, high transparency, and good mechanical properties simultaneously is of great significance but remains a challenge. In this work, a surface modification method combing nonsolvent induced phase separation (NIPS) and liquid injection is proposed for the treatment of cellulose diacetate (CDA). It is discovered that by utilizing acetone/ethanol as the solvent system for NIPS, and carefully tuning CDA concentration, CDA films with controlled micro/nanoporous surface structures are obtained. Further injecting liquid paraffin into the porous surfaces, high transparent CDA films are achieved, with optical transmittance up to 91.8% (very close to 93% for the pure CDA film) in the visible range. Besides, the surface treatment also significantly changes the surface wettability, leading to hydrophobic CDA films (water contact angles increase from 58.2 to 106.6°) with good water-repelling and self-cleaning functions. Moreover, these surface-modified CDA films also have comparable or even more superior mechanical properties over the pure CDA film, with the tensile strength and the elongation at break as high as 45.2 MPa and 61.2%, respectively. This work would provide significant guidance for the large-scale preparation of CA-based films with special surface wettability, high transparency, and good mechanical properties.