The invention discloses a rare earth element modified ferro-aluminum-based fluorine removal agent and a preparation method thereof. The fluorine removal agent is composed of an aluminum-iron base material and a rare earth composite modified material, wherein the mass ratio of the aluminum-iron base material to the rare earth composite modified material is 100: (1-5); the ferro-aluminum base material is composed of activated aluminum oxide, aluminum salt and ferric salt, and the mass ratio of the activated aluminum oxide to the aluminum salt to the ferric salt is (3-5): (10-18): (5-8); the rare earth composite modified material is rare earth element chloride. The aluminum-iron-based fluorine removal agent is simple in production process, the prepared rare earth element chloride can be directly used without separation and purification, the production cost is greatly reduced, the prepared rare earth element modified aluminum-iron-based fluorine removal agent can be used for deep treatment of fluorine-containing wastewater, the fluorine removal effect is remarkable, and the method is suitable for industrial production. Particularly, after the fluorine-containing wastewater with the fluorine ion concentration of below 8mg/L is deeply treated, the fluorine removal rate can reach 90.79% at most.