The invention discloses a hydrophobic aqueous polyurethane ink. The hydrophobic aqueous polyurethane ink comprises the following raw materials in parts by weight: 40-50 parts of a modified aqueous polyurethane emulsion, 15-20 parts of a filler, 18-26 parts of a pigment, 2-3 parts of chitosan, 20-30 parts of dilute acetic acid, 0.5-1 part of a defoaming agent, 0.5-1.5 parts of a dispersing agent, 0.1-0.5 parts of a leveling agent, and 0.1-1 part of a thickener. The invention also discloses a preparation process of the hydrophobic aqueous polyurethane ink. The method adopts the modified aqueouspolyurethane emulsion as a resin matrix, and adds a proper proportion of a filler, a pigment and an auxiliary agent, so that the ink has excellent hydrophobicity, weather resistance, chemical resistance and high temperature resistance; at the same time, a natural antibacterial agent chitosan is added, so that the ink has certain antibacterial property, also has degradability and is more environmentally friendly, the ink has the advantages of low production cost, water and abrasion resistance, good printing effect, environmental protection, and safety, and widens the application range of traditional polyurethane aqueous inks.