The invention provides a method for preparing a biological fertilizer by brown coal humic acid. With phanerochaete chrysosporium CICC40719 as a starting strain; 100-300ml solution containing 0.3% of KH2PO4, 0.15%g of MgSO4 7H2O, 0.01% of vitamin B1, 5% of pulverized brown coal and 94.54% of deionized water is inoculated with the phanerochaete chrysosporium, which is cultured by a shaking table atthe temperature of 28 DEG C for 96 hours to prepare a bacterial culture suspension I; another 100-300ml solution containing 0.3% of KH2PO4, 0.15%g of MgSO4 7H2O, 0.01% of vitamin B1, 10% of pulverized brown coal and 89.54% of deionized water is inoculated with 5% of the bacterial culture suspensionI to prepare a bacterial culture suspension II; another 100-300ml solution containing 0.3% of KH2PO4, 0.15%g of MgSO4 7H2O, 0.01% of vitamin B1, 15% of pulverized brown coal and 84.54% of deionized water is inoculated with 5% of the bacterial culture suspension II which is cultured by the shaking table to prepare a bacterial culture suspension III which is separated and purified to obtain a phanerochaete chrysosporium acclimatized strain. A culture medium is inoculated with the culture medium and cultured for 24 hours, and fermentation broth is prepared. The brown coal is pulverized by a pulverizer and sieved by a 30-mesh sieve to obtain pulverized coal, which is added with water for regulating the moisture content of the pulverized coal to 35-40%, 12-15% of ammonia water (wet basis), and 2% of rice hull (wet basis), the wet pulverized coal is stirred evenly, spread out indoors to a thickness of 8cm, and thermostatically cultured at the temperature of 28 DEG C for 30 hours, then sulfuric acid solution with 8% percentage concentration is used for neutralizing the degraded pulverized brown coal, the pH value of which is adjusted between 6.5 and 7.5, after being dried with hot air at the temperature of 55 DEG C and pulverized, the biological fertilizer is prepared.