The invention discloses a chitosan-fulvic acid compound fertilizer and a preparation method thereof. The compound fertilizer comprises chitosan, fulvic acid, nitric phosphate, urea, urea formaldehyde, diammonium phosphate, potassium sulphate, medium and trace elements and rare earth elements. In the preparation method, the medium and trace elements are chelated by taking chitosan and fulvic acid as chelating agents, and a chelated liquid is taken as a bonding agent for producing and granulating simultaneously. The invention has the advantages that: the chitosan-fulvic acid compound fertilizeris only applied once without additional application in the entire growing period of crops, so that the cost can be lowered, the labor productivity is lowered, the problems of slow fertilizing at an early stage and insufficient fertilizing at a later stage existing in an ordinary fertilizer are solved, mutual help is given in an emergency, and the utilization ratio of the fertilizer is increased; the medium and trace elements are chelated by using the chitosan and the fulvic acid respectively, so that the chelating efficiency of the medium and trace elements is increased, and the absorption and utilization ratio of crops on the medium and trace elements is increased; and the chelated liquid is taken as a granulating bonding agent, so that the granulating rate is high, the production efficiency is high, other bonding agents do not need to be added, and the cost is saved.