The invention discloses a selenium-rich chlorella based functional fish feed and a preparation method of the selenium-rich chlorella based functional fish feed, the selenium-rich chlorella based functional fish feed comprises a rapeseed dreg, a rice bran, a flour, a fish meal, a soybean meal, a compound mineral substance, multi-vitamins, monocalcium phosphate, choline chloride, and a selenium-richchlorella powder in the formula, and the selenium-rich chlorella powder is prepared by adding 2 mg/L sodium selenite into a BG-11 culture medium under the optimized condition, culturing, finally homogenizing and breaking a wall after enzymolysis. The high selenium accumulating capability and the organic selenium transforming capability of the chlorella are used, the selenium content of the feed and the proportion of the organic selenium are effectively increased, the safety and the bioavailability of the selenium are strengthened, the economic benefit is further increased while the physique of fish and the meat quality are improved, the increase of the selenium content of the culture medium also promotes the synthesis of astaxanthin of the chlorella, and the immunity of a fish body is improved. The organic selenium-rich fish provides the technical support for the industrial development of selenium-rich fish foods on strengthening the immunity of the human body and resisting aging andcancers.