Seed germination of plants with various acid-resistance display different responses to acid rain. To understand the reason why such differences occur, the effects of simulated acid rain (pH 2.5–5.0) on the activities of peroxidase (POD) and catalase (CAT) during seed germination of rice (), wheat (), and rape ( var. ) were investigated. Results indicated that the maximum change in activities of CAT and POD by acid rain treatment with different acidity and time in relation to the referent treatment without acid rain, was in the order: rice (28.8%, 31.7%) < wheat (34.7%, 48.3%) < rape (79.3%, 50.0%). The pH level for which the treatment with acid rain did not cause significant difference ( < 0.05) was in the order: rice (3.5) > wheat (4.0) > rape (5.0). Moreover, the change in activity of POD was higher than that of CAT, which showed that POD was more sensitive to acid rain stress than CAT. The difference in the ability of POD and CAT in removing free radicals was one reason why the germination indexes of these three species behaved differently.