Fengguo Temple in Yixian County, Liaoning Province, is in the first batch of national key cultural relic protection units, and the existing Yuan Dynasty murals in the Great Buddha’s Hall are exquisite in picture and rich in content and are of high artistic and historical value. However, under the influences of natural and human factors over the past nearly one thousand years, these exquisite murals have different degrees of disease, among which flocculent contaminants have strong particularity, and the harm to the murals is especially serious. Our experiments took this kind of disease as the research object. First, it was judged that the range of distribution of contaminants on the surface of the murals was extremely large, which was seriously harmful to the preservation of the murals. Then, the methods of infrared spectrometry, energy spectrometry and X-ray fluorescence analysis were used to determine that the two flocculent contaminants unique to the mural surface were moth cocoon silk and spider silk. Finally, through environmental monitoring and review on relevant historical data, it was speculated that the reasons for their occurrence should be closely related to the environment of preservation and historical restoration. The accumulation of flocculent contaminants can do foreseeable and continuous harm to the surface of the murals, so cleaning up and prevention is extremely urgent. For the first time, a systematic analysis of flocculent contaminants of temple murals was conducted, with the aim of comprehensively revealing the characteristics and causes of flocculent contaminants on the surface of Yuan Dynasty murals in the Great Buddha’ Hall of Fengguo Temple. This work provides examples for research on the surface contaminants of temple murals and a certain theoretical basis for the exploration of targeted methods for cleaning and preventing contaminants on the surface of murals.