To understand the differential effects of altitudinal gradient on soil inorganic nitrogen concentration and associated ammonia-oxidizingbacteria (AOB) and archaea (AOA), intact soil cores from a primary coniferous forest were in situ incubated in an alpine forest at a 3582-m altitude (A1) and transplanted to subalpine forests at a 3298-m altitude (A2) and 3023-m altitude (A3) on the eastern Tibetan Plateau. Transplant cooled the soil temperature of A2 but warmed the A3 soil temperature. Both AOA and AOB were found at the three altitudes. Compared to A1, A2 had greater AOA and AOB abundance, but A3 showed lower AOA abundance in organic soil. The AOA abundance was negatively correlated with ammonium concentration at all three altitudes, but AOB showed the reverse trend. Our results suggested that the soil nitrogen process responded differentially to soil core transplanting at different altitudes.