The invention relates to humic acid biological fertilizer and a preparation method thereof and belongs to the field of fertilizer. The humic acid biological fertilizer is mainly prepared from the following raw materials in parts by weight: humic acid, a biological bacterium agent, auxin, cytokinin, active small peptide, potassium dihydrogen phosphate, potassium sulfate, urea, borax and a microcapsule enzyme. The biological bacterium agent is prepared from streptomyces jingyangensis, bacillus subtilis, trichoderma koningii, acetobacter diazotrophicus, pseudomonas fluorescens and pseudomonas chlororaphis. An enzyme in the microcapsule enzyme is prepared from nitrate reductase, metalloprotease and anti-oxidization dismutase. The humic acid biological fertilizer provided by the invention has abundant nutrient elements; the utilization rate of all nutrient substances is high and the humic acid biological fertilizer is applicable to various crops; the yield and quality of the crops can be effectively improved, and the humic acid biological fertilizer is green and environmentally friendly. The preparation method of the humic acid biological fertilizer comprises the step of mixing the rawmaterials according to the ratio. The method is simple and easy to operate and is suitable for industrial production.