The invention relates to a preparation method of carboxyl nitrile rubber through emulsion polymerization. According to the preparation method, acrylonitrile, an emulsifier, an adjusting agent, and an initiator are added into a polymerization kettle, then butadiene is added, emulsion polymerization is carried out under stirring, and in the late phase of emulsion polymerization, unsaturated carboxylic acid and / or anhydride thereof is added into the polymerization kettle. The obtained carboxyl nitrile rubber has a low content of gel and a two-layer molecular structure, the index of conjugated acid is controllable; during the processing process, a three-dimensional network structure can be easily formed, thus the mechanical and physical properties of rubber products made of the carboxyl nitrile rubber are good; after processing, the Mooney viscosity is increased, the crosslinking degree of finished products is good, and especially, the elongation at break is prominently improved.