Most historical sites in archaeological museums have an inorganic origin. According to the specifications prescribed in CIE 157: 2004, these inorganic collections are light-insensitive and can be preserved in an environment without any light restrictions. Roof skylights are therefore widely used in archaeological museums in China to provide natural lighting and reduce lighting energy consumption. However, many of the historical sites in these archaeological museums are not preserved as well as expected due to their unique soil-air coupled preservation environment and the transmission of sometimes intense sunlight into the relic preservation area. This research takes Chengdu Jiangnan Pavilion Street Site Museum as a case study to evaluate the influence of skylights and direct sunlight on historical sites within archaeological museums. An integrated analysis of the negative impact of skylights on historical sites was implemented by comparing the preservation environment in illuminated and non-illuminated areas. The results show that the light intensity at the illuminated area is more than 100 times at the non-illuminated area, the intense sunlight not only induces severe environmental fluctuations where the maximum daily change in temperature and RH reach 9.7 degrees C and 24%, respectively, but, under the damp conditions at this site, also accelerates salt accumulation at the site surface and stimulates moss growth. Strong sunlight through a skylight can result in deterioration even of light-insensitive historical sites within archaeological museums, and so skylights in archaeological museums should be rationally designed to avoid sunlight directly hitting the surface of historical sites housed within them.