Acid rain is a global environmental problem that threatens agricultural production. Calcium (Ca), as a signal substance for physiological activities, has been known to regulate plant growth under abiotic stresses. To clarify whether calcium could be one of possible ways to alleviate the reduction caused by acid rain in agricultural production and investigate its regulating mechanism on adaptation of plants under acid rain stress, we studied the effect of exogenous Ca2+ (5 mM CaCl2) on growth of soybean at different growth stages (seedling, flowering-podding, and filling stages) as well as yield and grain quality of soybean under simulated acid rain (pH 4.5 or pH 3.0) stress. We found that the application of Ca2+ could regulate the activity of plasma membrane H+-ATPase, for mitigating the increase of ammonium and the decrease of nitrate and phosphorus in soybean roots, which mitigated the inhibition on growth and improved the yield and grain quality of soybean under simulated acid rain stress. In addition, the alleviating effect of exogenous Ca2+ on soybean was the most significant at seedling stage. The results indicate that the exogenous Ca2+ could enhance the adaptation of soybean and facilitate the recovery of soybean productivity and grain quality under simulated acid rain stress by maintaining the uptake of nitrate, ammonium, and phosphorus.