Rainwater chemistry plays an important role in the earth-surficial ecosystem, but studies on rainwater chemical composition of karst agro-ecosystem are rare. To explore the rainwater alkalization and the provenance of components responsible for neutralization, two-years chemical monitoring of rainwater was carried out in a karst agricultural catchment in Southwest China. The main findings suggest that SO₄²⁻, NO₃⁻, Ca²⁺, and NH₄⁺ are the principal ions. All the ionic contents show distinctly seasonal variation (highest in winter) in response to variations in seasonal precipitation because the rain-scour process can efficiently remove atmospheric materials. Source identification indicates that Cl⁻ and Na⁺ are mainly derived from marine input whereas SO₄²⁻ and NO₃⁻ are controlled by anthropogenic emission, in particular, fixed emission sources. The source of NH₄⁺ is attributed to intense agricultural production, while Ca²⁺ and Mg²⁺ are mainly derived from calcite dissolution. The rainwater alkalization caused by the seasonal acid neutralization (via basic components, Ca²⁺ and NH₄⁺) is beneficial to crop growth but also reflect agricultural overfertilization. Sulfur controlled the total wet acid deposition (68%–94%) and could be a potential agent of weathering.