The invention discloses a double-source humic acid biological fertilizer and a preparation method and an application thereof. The double-source humic acid biological fertilizer takes ganoderma lucidum mushroom residue, arctium lappa leaves, weathered coal or peat, a conditioning agent, compound enzyme, and a composite inocula as main raw materials, the double-source humic acid biological fertilizer is produced through enzymatic hydrolysis and microbial fermentation, and the steps also comprise chemical activation of weathered coal or peat, enzymatic hydrolysis of arctium lappa leaves, and uniform mixing with the ganoderma lucidum mushroom residue, and fermentation decomposition by using the composite inocula. The double-source humic acid biological fertilizer comprehensively uses the ganoderma lucidum mushroom residue and the arctium lappa leaves, biological humic acid and ore-source humic acid in the biological fertilizer are subjected to synergistic interaction, and the double-source humic acid biological fertilizer has the functions of improving soil, promoting plant growth, enhancing disease-resistant and stress-resistant capabilities, and increasing the product quality effect.