The invention provides a temperature control method and a temperature control system for hydrogen energy source filling of a hydrogen refueling station. The method comprises the following steps: S10,obtaining a hydrogen energy source compressed by a compressor and cooling the hydrogen energy source for the first time; S20, filling the hydrogen energy source cooled for the first time to a buffer bottle; and S30, filling the hydrogen energy source cooled for the first time to to-be-hydrogenated equipment through the buffer bottle. By conventionally cooling the hydrogen energy source compressedby the compressor and filling the hydrogen energy source to the to-be-hydrogenated equipment through the buffer bottle, a temperature rise problem generated in the hydrogen energy source filling process is solved by cooling the hydrogen energy source by gas for many times and reducing the pressure difference by way of gas pre-cooling and stepped and overlapped filling in the process of filling thehydrogen energy source to the to-be-hydrogenated equipment, so that the hydrogenation risk is reduced.