The invention provides a multifunctional organic/inorganic compound fertilizer and a preparation method thereof. The compound fertilizer is composed of the following raw materials by weight percent: 25-30% of urea, 5-10% of monoammonium phosphate, 10-18% of potassium sulphate, 27-32% of humic acid, 1.5-3% of zinc sulfate, 0.1-0.3% of microorganism bacterial liquid, 12-20% of diatomite and 1.9-2.7% of sophorolipid, wherein humic acid is obtained from decomposed coal through activation treatment. During preparation, urea, monoammonium phosphate, potassium sulphate, humic acid, zinc sulfate, microorganism bacterial liquid, diatomite and sophorolipid are added to a mixing crusher for crushing, so that a powdery mixture is obtained; the powdery mixture is added to a drum coating-pelleting-drying-cooling integrated machine to be pelleted, dried and cooled so that a granular mixture is obtained; the microorganism bacterial liquid and the diatomite are mixed and then sprayed to the mixture so that a crude product of the multifunctional organic/inorganic compound fertilizer is obtained; and finally, the crude product is added to a vibrating sieve for screening and then the obtained oversize is the multifunctional organic/inorganic compound fertilizer.