The invention relates to a method for preparing a slow-release synergistic brown algae urea-ammonium mixed nitrogen fertilizer by compound microorganism fermentation. The method comprises the following steps: immersing fresh brown algae and pulp-refining, preparing a seed broth of a bacterial strain, inoculating the seed broth into the brown algae bed material for many times, realizing graded fermentation, preparing brown algae functional inocula from the fermentation product, combining the brown algae functional inocula and chemical fertilizer feedstock through a mild reaction type granulating process, and finally obtaining the slow-release synergistic brown algae urea-ammonium mixed nitrogen fertilizer rich in brown algae extract and special-efficacy composite bacterial strain. Experiments show that the composite graded fermentation technology has more excellent effects than single strain fermentation. The prepared brown algae urea-ammonium mixed nitrogen fertilizer has obviously higher fertilizer efficiency than a traditional urea-ammonium mixed nitrogen fertilizer.