The invention relates to the technical field of directional arraying agents, specifically to a directional arraying agent for a waterborne effect pigment, and a preparation method and application thereof. The directional arraying agent for the waterborne effect pigment comprises the following raw materials by weight: 10 to 50 parts of monomer, 1 to 10 parts of an emulsifier, 0.5 to 5 parts of an initiator and 50 to 100 parts of deionized water. The preparation method comprises a first step of emulsifying the monomer, the emulsifier, the initiator and deionized water in a reaction vessel and a second step of carrying out free radical polymerization so as to obtain the directional arraying agent for the effect pigment. The waterborne directional arraying agent has zero VOC discharge; the waterborne effect pigment can be directionally arrayed in paint and presents strong metal sensation; and the preparation method is simple in process and favorable for large-scale production. Excellent flashing effect can be obtained by only adding 0.2 to 3% of the directional arraying agent for the waterborne effect pigment into waterborne paint.