The invention discloses a rubber composition containing an organic acid-zinc-phenolic resin compound, and a preparation method and an application thereof. The rubber composition includes 100 parts ofrubber, 1.0-30.0 parts of the organic acid-zinc-phenolic resin compound, 40.0-120.0 parts of carbon black and 3.0-10.0 parts of sulfur, and also contains processing oil, a vulcanization promoter, a methylene donor and other additives. Coordination crosslinking bonds formed by the organic acid-zinc-phenolic resin compound can increase the strength and the heat resistance of phenolic resin, the structure of the organic acid can also increase the compatibility of the phenolic resin with the rubber, and the compound can improve the reinforcing effect of the phenolic resin, so the rubber composition has the characteristics of high modulus, low initial Mooney viscosity, prolonged fatigue life, and outstanding mechanical properties after high temperature aging.