<p>Acid rain worldwide severely inhibits agricultural productivity to threaten global food security. As for the short-term, hardly any measures are feasible to stop the source of acid rain, alternatives are searched to reduce its agricultural damage. Calcium (Ca²⁺) is a known intracellular messenger to regulate plant tolerance to abiotic stresses, but few information is available for clarifying formation of Ca²⁺ signatures in plants under acid rain stress. Therefore, we studied effect of exogenous Ca²⁺ on intracellular Ca²⁺ homeostasis in <i>Oryza sativa</i> roots under stimulated acid rain stress. Stimulated acid rain at (pH 4.5 or 3.0) promoted extracellular Ca²⁺ influx by upregulating expression of <i>OsANN3</i>, <i>OsCNGC9</i>, <i>OsCNGC13</i>, <i>OsTPC1</i> and <i>OsMAC1</i>. Meanwhile, heavier stimulated acid rain (pH 3.0) hindered Ca²⁺ efflux by inhibiting activities of Ca²⁺/H⁺ transporter and Ca²⁺-ATPase, and then disrupted intracellular Ca²⁺ homeostasis, causing irreversible damage to plasma membrane stability and growth in rice. Exogenous Ca²⁺ not only promoted extracellular Ca²⁺ influx to format Ca²⁺ signal, and alleviated the inhibition of acid rain at pH 3.0 on intracellular Ca²⁺ efflux to restore intracellular Ca²⁺ homeostasis, benefiting to maintaining plasma membrane stability and growth in rice. In addition, the alleviating effect of exogenous Ca²⁺ on plasma membrane Ca²⁺-ATPase activity was mainly resulted from regulating the expression of <i>OsACA2</i> and <i>OsACA4</i>, phosphorylation of P-type IIB Ca²⁺-ATPase and calmodulin concentration. Our findings demonstrate that regulation of exogenous Ca²⁺ on maintaining intracellular Ca²⁺ homeostasis could be one of causes for enhancing rice tolerance to acid rain. It may provide new perspective for developing ways to alleviate inhibition of acid rain on agricultural productivity.</p>