Trace metals can enter natural regions with low human disturbance through atmospheric circulation; however, little information is available regarding the filtering efficiency of trace metals by forest canopies. In this study, a representative subalpine spruce plantation was selected to investigate the net throughfall fluxes of eight trace metals (Fe, Mn, Cu, Zn, Al, Pb, Cd and Cr) under a closed canopy and gap-edge canopy from August 2015 to July 2016. Over the one-year observation, the annual fluxes of Al, Zn, Fe, Mn, Cu, Cd, Cr and Pb in the deposited precipitation were 7.29 kg·ha−1, 2.30 kg·ha−1, 7.02 kg·ha−1, 0.16 kg·ha−1, 0.19 kg·ha−1, 0.06 kg·ha−1, 0.56 kg·ha−1 and 0.24 kg·ha−1, respectively. The annual net throughfall fluxes of these trace metals were −1.73 kg·ha−1, −0.90 kg·ha−1, −1.68 kg·ha−1, 0.03 kg·ha−1, −0.03 kg·ha−1, −0.02 kg·ha−1, −0.09 kg·ha−1 and −0.08 kg·ha−1, respectively, under the gap-edge canopy and 1.59 kg·ha−1, −1.13 kg·ha−1, −1.65 kg·ha−1, 0.10 kg·ha−1, −0.04 kg·ha−1, −0.03 kg·ha−1, −0.26 kg·ha−1 and −0.15 kg·ha−1, respectively, under the closed canopy. The closed canopy displayed a greater filtering effect of the trace metals from precipitation than the gap-edge canopy in this subalpine forest. In the rainy season, the net filtering ratio of trace metals ranged from −66.01% to 89.05% for the closed canopy and from −52.32% to 33.09% for the gap-edge canopy. In contrast, the net filtering ratio of all trace metals exceeded 50.00% for the closed canopy in the snowy season. The results suggest that most of the trace metals moving through the forest canopy are filtered by canopy in the subalpine forest.