The present invention discloses a two-stage hydrotreating method of a poor-quality raw material. According to the two-stage hydrotreating method, a poor-quality raw material firstly enters a first-stage reaction zone to carry out a hydrorefining reaction, a gas-liquid co-current flow process and a gas-liquid counter flow process are concurrently adopted in the first-stage reaction zone, and the generated oil obtained in the first-stage reaction zone enters a second-stage reaction zone to carry out a deep denitrogenation and aromatic hydrocarbon saturation reaction. With the method of the present invention, the nitrogen-containing impurities in the poor-quality raw material can be subjected to hydrotreating under the relatively mild condition so as to make the poor-quality raw material meet the catalytic cracking raw material requirement, such that the hydrotreating raw material source is broadened; and the hydrorefining temperature is substantially reduced so as to increase the operation period of the device and process the poor-quality raw material, or increase the processing capacity of the device in the same operation period.