Chlorophyll content and fluorescence parameters can reflect the chloroplast state and photosynthesis efficiency, and can be used to study the adaptability and response mechanism of plants to the environment. In this study, the Salaxi Rocky Desertification Control Demonstration Area in Bijie City, Guizhou Province was selected as the research area. In total 168 epilithic moss specimens were collected to explore the responses of their relative chlorophyll content (SPAD value) and chlorophyll fluorescence parameters to habitats of different rocky-desertification grades (none, potential, light, moderate and severe). The results showed that:(1) the SPAD value, chlorophyll fluorescence parameters of epilithic mosses were comprehensively influenced by many environmental factors, among which the effects of rocky desertification grade, slope direction, canopy density, and atmospheric temperature were more significant. (2) Compared with habitats of lower grades of rocky desertification and shady slope, the SPAD value and chlorophyll fluorescence parameters except non-photochemical quenching coefficient (NPQ) and non-regulated energy dissipation (Ф_NO) of epilithic mosses decreased in medium and high-grade rocky desertification habitats and sunny slopes. It might hint that, in the later stage of rocky desertification degradation, the chlorophyll content of epilithic mosses decreased, the activity of reaction centers was affected, PSⅡ electron transport of was blocked, self-protection function was meantime activated thorough a non-regulatory mechanism as well as increasing heat dissipation. (3) Among the three dominant epilithic mosses, Erythrodontium julaceum had significant lower SPAD values than Gollania tereticaulis and Cyrto-hypnum gratum. For each moss, there was no significant change in habitats of different rocky desertification grades. It indicated that the response of moss chlorophyll content to the habitat degradation might be through species selection rather than adjustment and adaptation of the same species. (4) With the degradation of rocky desertification habitat, chlorophyll fluorescence parameters of G. tereticaulis did not change significantly except the significant increase of NPQ, indicating that G. tereticaulis kept relatively high and stable photosynthesis efficiencies in different rocky desertification areas. Both E. julaceum and C. gratum showed relatively significant changes and photo-inhibition occurred in higher-level rocky-desertification habitats, which initiated different protective mechanisms. Compared to other two dominant moss species, G. tereticaulis has larger biomass, covering a large area of rock surface in some plots. In addition of stronger photosynthetic capacity, it is more adaptive to higher-level rocky-desertification habitats. Therefore, G. tereticaulis might have potential to be used on research of bare-rock restoration in rocky desertification regions. The results can provide certain data support and theoretical basis for the study of rocky desertification ecosystem and its vegetation restoration mechanisms.