The invention provides a preparation method of a carbon-nanotube-based fuel cell catalyst. The preparation method comprises the followings steps that a nitrogen-containing carbon source and non-noblemetal salt are provided, and the non-noble metal salt at least comprises ferric salt; the nitrogen-containing carbon source and the non-noble metal salt are mixed to obtain a hybrid precursor; the hybrid precursor is subjected to heat treatment in a protective atmosphere; the hybrid precursor subjected to heat treatment is subjected to ammonia treatment in an ammonia atmosphere, and the carbon-nanotube-based fuel cell catalyst is obtained. According to the carbon-nanotube-based fuel cell catalyst prepared through the preparation method, multilayered structure regulating and controlling can beachieved, structures capable of being regulated and controlled comprise hole structures, graphitization degrees, active sites and the like; the carbon-nanotube-based fuel cell catalyst shows the excellent oxygen reduction property under the different pH conditions, and simultaneously shows the extremely-high stability especially under the alkaline condition; and in addition, synthetic raw materials used in the catalyst are rich in source and low in cost, and the requirements of commercial production for 'low cost' are met.