To better assess environmental impact of Northern Sea Route (NSR), the fuel carbon intensity of a ship fuel was established to analyze the feasibility of replacing Suez Canal Route (SCR) with NSR as alternatives. The Northern Sea Route (NSR) with good navigation conditions was selected. Taking the container transportation from Shanghai to Rotterdam as an example, the carbon intensity of NSR and SCR fuel for ship navigation was compared and analyzed. By setting four variables, such as different ship types, speed, cabin utilization and the proportion of segment distance in NSR common waters, the differences of ship navigation fuel carbon intensity between SCR and NSR were compared. The results show that under existing condition, compared to 16 000 TEU ordinary container ship on SCR, although iceclassed ships of all selected seven types on NSR can reduce carbon dioxide emission per single trip, however, only 14 000 and 16 000 TEU iceclassed NSR container ships can slightly reduce fuel carbon intensity, and the advantage was not great. The carbon intensity of navigation fuel for large container ships is lower. Reducing the ice water speed and improving the cabin utilization can reduce the fuel carbon intensity of ships sailing in NSR. The conclusion can provide reference for ship selection and speed setting in the NSR from the perspective of “carbon neutralization”. At the same time, the established fuel carbon intensity model can be extended to other routes.