The invention provides a method for preparing an acid organic fertilizer by orientation fermentation of an organic waste. The method is characterized by comprising the following specific steps of: mixing bacillus subtilis, bacillus licheniformis, bacillus pumilus, saccharomyces cerevisiae, acetobacter aceti, trichoderma, aspergillus oryzae, nocardia and geotrichum candidum to obtain a first composite microbial bacteria agent; mixing the bacillus subtilis, the bacillus licheniformis, the saccharomyces cerevisiae, bacillus coagulans, lactobacillus acidophilus, lactobacillus plantarum, lactobacillus casei, pediococcus pentosaceus, the aspergillus oryzae, mucor racemosus and the nocardia to obtain a second composite microbial bacteria agent; adding the first composite microbial bacteria agentinto the organic waste and performing aerobic fermentation so as to form an intermediate fermentation product; and adding the second composite microbial bacteria agent into the intermediate fermentation product and performing anaerobic fermentation so as to form the organic fertilizer. The method has the advantages of capability of improving saline and alkaline lands, suitability for cultivation of acidophilous crops, effect of performing micro-ecological remediation on continuous cropping soil and low cost.