Foxing spots are reddish-brown, brown, or yellowish spots in irregular shapes that are commonly discovered on paper materials. Effects of such foxing spots on degradation of Chinese papers have rarely been reported. In this study, a 20th century Chinese manuscript with few foxing stains was examined to explore the cause of stain formation. The paper areas with foxing stains were more acidic than those without the stains, while no obvious differences in cellulose crystallinity and iron and copper contents were observed when comparing paper areas with and without foxing spots via X-ray diffraction (XRD) and energy-dispersive X-ray fluorescence spectroscopy (ED-XRF), respectively. For further exploration, few fungal hyphae and spores in various sizes were observed using SEM, leading to increased mean roughness of the paper surface for the foxed area. This is further supported by the presence of amide II in the foxed area only, as detected via attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy. Fungal culture was then carried out to demonstrate that fungi belonging to the genera Alternaria tenuissima and Alternaria solani were present. This research provides an improved understanding of the effects of foxing spots on Chinese archives and informs of further conservation efforts.