A lithography system and a cleaning method thereof are provided. The lithography system includes a light source generator. The light source generator includes a collector, a droplet generator and a droplet catcher. The droplet generator and the droplet catcher are facing each other, and disposed at a region surrounding the collector. The cleaning method includes: shifting the droplet generator out of the light source generator via a port of the light source generator; inserting a shove assembly into the light source generator via the port; using a borescope attached to the shovel assembly to identify a location of a deposit formed by droplets generated by the droplet generator; using the shovel assembly to remove and collect the deposit; and withdrawing the shovel assembly along with the borescope from the light source generator via the port.