Carbon contamination on extreme ultraviolet (EUV) optics has been observed in EUV lithography. In this paper, we performed in situ monitoring of the build-up and removal of carbon contamination on Mo/Si EUV multilayers by measuring the secondary electron yield as a function of primary electron energy. An electron beam with an energy of 2 keV was used to simulate the EUV radiation induced carbon contamination. For a clean EUV multilayer, the maximum secondary electron yield is about 1.5 electrons per primary electron at a primary electron energy of 467 eV. The maximum yield reduced to about 1.05 at a primary electron energy of 322 eV when the surface was covered by a non-uniform carbon layer with a maximum thickness of 7.7 nm. By analyzing the change in the maximum secondary electron yield with the final carbon layer thickness, the limit of detection was estimated to be less than 0.1 nm.