The invention discloses a water-based sealing protecting agent for a coloured pavement and application thereof. The water-based sealing protecting agent for the coloured pavement comprises a multicolour asphalt composite emulsion, a colour paste and a water-based finishing agent; the colour paste comprises organic toner or inorganic ferric oxide toner series; the water-based finishing agent comprises an organic silicon-modified acrylate emulsion, a dispersing agent, an anti-foaming agent and a water-soluble anti-ultraviolet absorbent. The water-based sealing protecting agent for the coloured pavement is mainly prepared by the multicolour asphalt composite emulsion and the colour paste, but is matched with the water-based finishing agent. The water-based finishing agent is added into a mixed material consisting of the multicolour asphalt composite emulsion and the colour paste, chemical bonding can be produced to form enhanced fibres in reaction, and the interface bonding is also enhanced so that the interface breaking energy is also improved. Therefore, a pavement which has an integrated cementing structure with excellent continuity, quick curing and balanced rigidity and toughnessis formed. Moreover, according to a construction design requirement, different colour paste can be selected and added, so that ultrathin coloured coating surfaces with different colours can also be formed.