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Ammonia plays a key role in the neutralization of atmospheric acids such as sulfate and nitrates. A few in situ observations have supported the theory that gas-phase NH3 concentrations should decrease sharply with altitude and be extremely low in the upper troposphere and lower stratosphere (UTLS). This theory, however, seems inconsistent with recent satellite measurements and is also not supported by the aircraft data showing highly or fully neutralized sulfate aerosol particles by ammonium in the UTLS in many parts of the world. Here we reveal the contributions of deep convective clouds to NH3 in the UTLS by using integrated cross-scale modeling, which includes molecular dynamic simulations, a global chemistry transport model, and satellite and aircraft measurements. We show that the NH3 dissolved in liquid cloud droplets is prone to being released into the UTLS upon freezing during deep convection. Because NH3 emission is not regulated in most countries and its future increase is likely persistent from agricultural growth and the warmer climate, the effect of NH3 on composition and phase of aerosol particles in the UTLS can be significant, which in turn can affect cirrus cloud formation, radiation, and the budgets of NOx and O3.