The invention discloses a waterborne epoxy coating for containers and a preparation method of the waterborne epoxy coating. The waterborne epoxy coating comprises a host and a curing agent according to a mass ratio of 2.3:1. The host comprises deionized water, anti-settling agents, amine adduct, wetting dispersants, first defoamers, pigment, packing, coalescing agents, second defoamers, base wetting agents, flatting agents and thickeners. The curing agent comprises epoxy emulsion, deionized water, second defoamers and in-can preservatives. The preparation method of the waterborne epoxy coating for containers includes steps of (1), preparation of the host; (2), preparation of the curing agent; and (3), blending the host with the curing agent according to the mass ratio of 2.3:1. The coating has low volatile organic content (smaller than 60g/L) and high environment-friendly property, the coating can be dried at a high speed (namely the surface drying time is lower than 20 minutes at the room temperature), and requirements of high production efficiency of a container production line can be met completely.