Moss is an essential component in most forest ecosystems, and plays critical roles in material cycling and water retention. It is also an indicator of environmental change. An increasing numbers of studies have demonstrated that the growth and reproduction of mosses can be determined by light regime, substrate, and hydro-thermal dynamics. Theoretically, a forest gap might improve the growth and element uptakes by mosses on different growth substrates by altering the light regimes and the temperature and moisture dynamics on the forest floor through the redistribution of light and precipitation. As yet, the effects of forest gap position on microelement uptakes by mosses on different growth substrates remain unclear. To understand the effect of gap regeneration on microelement uptakes by mosses, the concentrations of sodium (Na), zinc (Zn), magnesium (Mg), manganese (Mn), calcium (Ca), and iron (Fe) in epilithic and epigeic mosses, and in the soil organic and mineral soil layers were investigated in open areas, the gap center, the gap edge, and the closed canopy in an alpine fir (Abies faxoniana) forest in western Sichuan during October 2016. No significant differences for the concentrations Na, Zn, Mg, Fe, and Ca were recorded between epilithic mosses and epigeic mosses, while the Mn concentration in epigeic mosses were significantly higher than those in epilithic mosses. The Zn, Mg, Mn, and Ca concentrations in the soil organic layer were significantly higher than the mineral soil layer, but the Fe concentrations in the mineral soil layer were significantly higher than the soil organic layer. However, no significant difference was observed in Na concentrations between the soil organic layer and the mineral soil layer. Gap positions had similar effects on the concentrations of Na, Zn, Ca, and Fe in epilithic mosses and epigeic mosses, and the mosses in the gap center and open areas had higher Na, Zn, Ca, and Fe concentrations. In contrast, different responses to gap positions were found in Mn concentrations between epilithic and epigeic mosses. Higher Mn concentrations in epilithic moss were found in the microenvironment under the closed canopy, whereas higher Mn concentrations in epigeic moss were observed in the gap center microenvironment. However, gap positions had only slight effects on Mg concentrations in moss plants. Forest gap positions had similar effects on microelement concentrations in the soil organic layer and mineral soil layer. Higher Na concentrations in the soil organic and mineral soil layers were found in the open area, while higher Zn, Mn, Ca, and Fe concentrations in the soils were found at the gap center. The lowest concentrations of the measured microelements in the soil organic and the mineral soil layers were found at the gap edge. In addition, the Na, Zn, Mn, and Ca concentrations in epigeic mosses were significantly higher than those in the corresponding soils, while the Fe concentrations showed an opposite trend. Furthermore, the Ca and Mn concentrations in moss plants correlated positively and significantly with the Ca and Mn concentrations in the corresponding soils. In conclusion, gap regeneration affects microelement sequestration by mosses and soils in an alpine forest, which provides new insights into the roles of forest gap regeneration and mosses on bioelement cycles in the alpine forest ecosystem.