The invention discloses an organic fertilizer dedicated for a navel orange tree and a preparation method thereof. The organic fertilizer dedicated for the navel orange tree is prepared from the ingredients: chicken manure, cow dung, bran powder, corn meal, humic acid, a fermentation agent, bacillus subtilis, rhizobia, actinomycetes, lactic acid bacteria, antagonistic bacteria, protease, cellulase, calcium superphosphate, boric acid and zinc sulfate monohydrate. The preparation method of the organic fertilizer dedicated for the navel orange tree is characterized by comprising the following steps: evenly mixing the bacillus subtilis, the rhizobia, the actinomycetes, the lactic acid bacteria, the antagonistic bacteria, the protease, the cellulase, the corn meal, the boric acid and the zinc sulfate monohydrate for later use; evenly mixing the chicken manure, the cow dung, the bran powder, the calcium superphosphate, the humic acid and the fermentation agent; fully and evenly mixing the microbial inoculum obtained in the first step and materials obtained in the second step; then stacking and turning over, and testing the temperature every day; turning over again when the stacking temperature reaches 75 DEG C and is maintained for 48 hours; after the temperature of the materials is about to reach 30 DEG C, ending the fermentation of the materials; crushing and sieving the fermented materials, and finally packaging.