The invention discloses a preparation method of a composite alga fertilizer. The preparation method comprises following steps: step one, preprocessing alga to obtain alga particles; step two, dissolving alga particles by distilled water to obtain an alga colloidal solution; step three, carrying out enzymatic hydrolysis; step four, subjecting the mixed solution to centrifugation, collecting the supernate, placing supernate in a vacuum freeze-drying machine, and dehydrating the supernate to obtain alga powder; step five, preparing a strain fermenting liquid; and step six, slowly adding the strain fermenting liquid into the alga powder to form a fermentation heap, carrying out fermentation for 14-20 hours, pushing over the fermentation heap, building a new fermentation heap, repeating for 5-6times, and then paving the fermentation heap to obtain the composite alga fertilizer. The preparation method has the advantages that alga is processed by an enzymatic hydrolysis method, the effectivecomponents of alga such as nutrients, plant hormones, and the like can be maximally maintained; moreover, the alga colloidal solution is enzymatically hydrolyzed under an acidic condition, the effectof the enzymatic hydrolysis is better, the enzymatic hydrolysis quality is higher, the raw material utilization rate is increased, the production cost is reduced, and the production quality is improved.