The invention discloses preparation methods of a compound fermenting microbial agent and a water-soluble fish protein amino acid fertilizer. The preparation methods include: 1) mixing facultative anaerobic bacillus, aerotolerant anaerobic lactobacillus and obligate anaerobic Bifidobacterium to form the compound fermenting microbial agent; 2) mixing corn starch, ammonium tartrate, disodium hydrogenphosphate, glucose, the compound fermenting microbial agent and water, stirring evenly, and activating the compound fermenting microbial agent; 3) smashing fish, shellfish, aquatic product processingleftovers into homogenate, removing impurities, quantitatively adding the homogenate into a fermentation tank, adding the activated compound fermenting microbial agent, which accounts for 0.2-5wt% ofthe homogenate, into the fermentation tank, mixing the activated compound fermenting microbial agent and the homogenate evenly, sealing the fermentation tank, and standing at normal temperature for 10-15 days to obtain fermented mash; 4) filtering the fermented mash with a filter to obtain fermented liquid which is fish protein amino acid fermented liquid; 5) adding at least one of following microelements including copper, iron, manganese, zinc, boron and molybdenum to prepare the required water-soluble fish protein amino acid fertilizer.