Acid rain is a global environmental problem. Acid rain can affect plants directly by damaging the leaves and indirectly by soil acidifying. Many studies have been conducted to investigate the impacts of acid rain on plant under a single soil type. However, there is little information on the effect of acid rain on plant under different soil types. Jatropha curcas L. is an energy plant widely distributed in acid rain pollution area with various soil types. In this study, we investigated the effects of acid rain (pH2.5, pH3.5, pH4.5, pH5.6) on the growth, physiology, nutrient elements and bacterial community of J. curcas seedlings under different soil types [Red soils (RS), Yellow soils (YS), Yellow-brown soils (YBS), and Purplish soils (PS)]. Acid rain and soil types significantly influence the growth of J. curcas seedlings, and there was a significant interaction between acid rain and soil types. Acid rain (pH 4.5) was beneficial to the growth of J. curcas seedlings, whereas acid rain (pH 2.5 or 3.5) inhibited growth of J. curcas seedlings. The growth of J. curcas seedlings could resist the stress of acid rain by scavenging and detoxification of active oxygen species in leaves. Combined with the increase in relative growth rate of seedlings treated with simulated acid rain at pH 4.5, we inferred that K can stimulate the growth of seedlings. The lower soil pH, cation exchange capacity and base saturation had stronger inhibitory effects on growth of J. curcas seedlings. YBS and PS were beneficial for growth of J. curcas seedlings by higher buffering capacity under acid rain treatments. The phylum Proteobacteria was found to predominate in rhizosphere soils. YBS was favorable to support Proteobacteria growth and reproduction. The redundancy analysis showed that the Cyanobacteria were favorable to growth of J. curcas seedlings.