The present invention belongs to the technical field of seaweed fertilizers, and particularly relates to a seaweed oligosaccharide micro-ecology drip irrigation fertilizer, which comprises, by weight, 10-60% of a seaweed oligosaccharide solution, 10-50% of a molasses solution, 20-40% of a composite microorganism bacterial solution, and 10-40% of large, medium and trace elements, wherein crushed seaweed and water are mixed, a biological lyase is added to carry out enzymolysis so as to obtain a seaweed enzymolysis liquid, and extraction and pressure filtration are performed under an alkaline condition so as to obtain the seaweed oligosaccharide solution. The invention further provides a preparation method of the seaweed oligosaccharide micro-ecology drip irrigation fertilizer. According to the present invention, the effective component in the seaweed is substantially retained, the utilization rate of crops on the nutrients can be substantially improved, the preparation period is substantially shortened, the necessary organic matter and the trace elements can be supplemented, the composite microorganism bacterial solution is added, functions of disease resistance, stress tolerance, phosphorus dissolving, potassium dissolving, and soil physical structure increasing are provided, and various types of soil-borne diseases can be effectively prevented and controlled.