Ammonia (NH3) emission reduction is key to limiting the deadly PM2.5 pollution globally. However, studies of long-term source apportionment of vertical NH3 are relatively limited. On the basis of the one-year measurements of weekly vertical profiles of δ15N-NH3 at 5 heights (2, 15, 102, 180, and 320 m) on a 325-m meteorological tower in urban Beijing, we found that vertical profiles of NH3 concentrations generally remained stable with height. δ15N-NH3 increased obviously as a function of height in cold seasons (with heating) and decreased in warm seasons (with fertilization), indicating a stronger human-induced seasonal variation via regional transport at higher altitudes. Relatively stable δ15N-NH3 near the ground surface suggested the strong local emission. The results of isotopic mixing model (SIAR) indicate that source apportionment using measured δ15N-NH3 only would overestimate the contribution of agricultural emissions to NH3. By using an estimation of initial δ15N-NH3, we found that nonagricultural sources contributed ∼72% of NH3 on average. Our study suggests that (i) both persistent nonagricultural and periodic agricultural emissions drive atmospheric NH3 concentration and its vertical distribution in urban Beijing; and (ii) source apportionment based on measured δ15N-NH3 only likely underestimates fossil fuel source contribution, if the combined NHx isotope effects are not considered.