The invention discloses a pollution-free electron multiplier assembly system and an assembly method thereof. In the scheme, a vacuum pumping system and a gas purifying system are used for maintaining working pressure and a gas environment all the time during assembly, so that an electron multiplier assembly process is conducted in a non-atmospheric environment, and pollution of the atmosphere to a dynode secondary electron emission surface can be reduced. Moreover, dynodes can be protected by continuously-flowing nitrogen flow. Additionally, all parts of an electron multiplier enter a main cabinet from a transition bin, the assembled electron multiplier is conveyed out of the main cabinet from the transition bin, and the transition bin is subjected to air purification before the parts in the transition bin enter the main cabinet, so that removing gas impurities carried by the parts in advance is guaranteed, and cleanliness of the working environment of the main cabinet is further guaranteed.