Aiming at the protection of aviation equipment, the waterborne protective coating system for aviation equipment is composed of waterborne epoxy resin coating with outstanding adhesion and excellent anti-corrosion performance as primer and acrylic polyurethane coating with strong abrasion resistance and durable weather resistance as topcoat. In this study, the design idea of protective coating system was put forward. The one-component primer of protective coating system was prepared by using polymer epoxy resin dispersion as base material resin. The two-component finish coating for protective coating system was prepared using waterborne acrylic resin dispersion with high hydroxyl content and waterborne polyurethane curing agent modified by organic silicon as base resin. The coating system construction performance research and coating performance test were finished. The waterborne protective coating can meet the actual construction conditions, and is suitable for aluminum alloy, carbon steel and other substrates. It has the characteristics of outstanding adhesion,high gloss and durable protection performance.