The invention discloses an organic compound fertilizer with citrus pomace and a preparation method of the organic compound fertilizer and belongs to the technical field of preparation of organic fertilizers. The preparation method comprises the following steps of reducing the acidity of the citrus pomace by adopting microbial fermentation for deacidification, decomposing nondegradable components such as pectin and cellulose in the citrus pomace by adopting a compound-enzyme preparation, carrying out composting fermentation by microbial liquid inoculant, finally adding batched materials such as urea, monoammonium phosphate and potassium sulfate, and carrying out insect killing, sterilization, granulation, drying, cooling, sieving, coating and packaging to prepare the organic compound fertilizer with rich organic matter and the contents of N, P and K meeting the need of the optimal proportion for growth of citrus. The organic compound fertilizer and the preparation method disclosed by the invention have the advantages that deacidifying yeast is adopted to reduce the acidity of the citrus pomace and replace the existing method for adding quick lime to carry out deacidification, calcification and alkalization of soil are effectively prevented, the content of the compound fertilizer is more than 55%, the pH value is 6.5-8.5, the total contents of N, P and K are more than or equal to 8%, the water content is less than or equal to 20%, the contents of trace elements such as B, Zn and Mg are rich, and the other quality indexes are superior to national standard of organic fertilizer respectively.