The invention provides a colored permeable pavement asphalt mixture, which is formed by mixing of modified asphalt, 100 mass parts of aggregate and a colored high viscosity additive. The modified asphalt and the colored high viscosity additive are 4.6-5.0 mass parts in total, and the mass ratio of the colored high viscosity additive to the modified asphalt is (8-12):(92-88), and the aggregate includes coarse aggregate, fine aggregate, mineral powder and toner. The invention also provides a preparation method and application of the colored permeable pavement asphalt mixture. Compared with the existing commercially available colored asphalt mixture and colored decolorized asphalt mixture, the mixture provided by the invention not only has bright color and excellent water permeability, but also has the pavement performance meeting the technical requirements of high-speed pavement, and can be used for paving of high-speed pavement surfaces, municipal pavements, service area pavements, plant area and park pavements, turning road sections, uphill and downhill roads, bus stops and pavements at tunnel entrances and exits.