The invention discloses a cationic compound waterborne polyurethane based black dye and a preparation method thereof. The preparation method comprises the following steps: mixing polypolyols and a hydrophilic chain extender, heating to 100 to 140 DEG C, and performing dehydration treatment for 1 to 2h under the condition that vacuum degree is less than or equal to 0.1Mpa; introducing nitrogen, cooling to 50 to 70 DEG C, adding polyisocyanate monomer and a catalyst, heating to 80 to 100 DEG C, and keeping the temperature for 2 to 4h; adding small molecular red, blue, purple and yellow dyes intoa solvent in sequence, dissolving, reacting at 50 to 90 DEG C for 6 to 12h, and adding an organic solvent to adjust viscosity; cooling to 10 to 30 DEG C, adding a salt-forming agent, emulsifying at high speed for 10 to 30min, adding deionized water, and dispersing at high speed for 10 to 30min; removing the organic solvent under a vacuum condition to obtain cationic compound waterborne polyurethane based macromolecular black dye emulsion. According to the preparation method, a trichromatic theory is utilized, and the red, blue, purple and yellow dyes are connected into a polyurethane chain bya combination technology, so as to prepare the dye; not only are the blackness and utilization rate of the dye improved, but also the dyeing property and color fastness of the dye are improved.