The invention discloses boiling-resistant aqueous composite ink and a preparation method thereof. The boiling-resistant aqueous composite ink mainly comprises raw materials including aqueous polyurethane resin, a pigment and water, and a surface wetting agent, a wetting dispersing agent and a defoaming agent are additionally added. The preparation method of the boiling-resistant aqueous composite ink comprises the following steps of: firstly, adding partial aqueous polyurethane resin into a stirring reaction kettle; secondly, slowly adding the surface wetting agent, the wetting dispersing agent and partial defoaming agent, and adding the pigment after stirring and dispersing; thirdly, stirring and dispersing at high speed, and grinding after dispersing; fourthly, adding the residual aqueous polyurethane resin and defoaming agent and stirring and dispersing, and adding the water until the required viscosity is obtained through regulation; and at last, stirring, dispersing, filtering and packaging. The boiling-resistant aqueous composite ink, provided by the invention, is prepared by taking the high-performance aqueous polyurethane resin as a connecting material, and has the advantages of good pigment dispersibility, wide use range, lower film forming temperature, better mechanical property of formed film, more uniform particle size distribution and the like, and can be used for soft retort packages.