The invention discloses a preparation method of a catalyst with a core-shell structure for a low-temperature fuel cell, belonging to the technical field of fuel cells. In the catalyst with the core-shell structure prepared with the preparation method, platinum is taken as a shell, a metal alloy consisting of more than one of metals including ruthenium, platinum, iron, cobalt, nickel, copper, tin, iridium, gold and silver is taken as an inner core, and the shell and the inner core are loaded on a carbon carrier. The preparation method comprises the following preparation steps of: reducing a metal chloride or a metal nitrate with a reducing agent, and forming a core on the carbon carrier with a large specific surface area; stabilizing the core; and precipitating Pt on a core layer with a impregnation reduction method, a high-pressure organic sol method, a microwave method or an electrodeposition process to form the catalyst with the core-shell structure. Due to the adoption of the preparation method, the utilization ratio of noble metal platinum is increased, the cost of an electro-catalyst is reduced effectively, and the methanol oxidizing capability and oxygen reducing activity of the obtained catalyst are increased by 10.8 times and 8.7 times in maximum respectively in comparison to the mass ratio and activity of a commercial JM4100Pt/C catalyst.