The increasing microplastics (MPs) pollution and continuous acid rain coincide in many areas of the world. However, how MPs interact with acid rain is still unclear. Herein, we conducted a microcosm experiment to decipher the combined effect of polyethylene (PE) MPs (1%, 5%, and 10%) and acid rain (pH 4.0) on the agricultural soil ecosystem of Southern China, in which edaphic property, microbial community, enzymatic activity and CO emission were investigated. The results showed that PE MPs significantly decreased soil water retention and nitrate nitrogen content regardless of acid rain. Soil total nitrogen significantly decreased under the co-exposure of 10% PE MPs and acid rain. However, PE MPs did not alter soil microbial biomass, i.e., the content of microbial biomass carbon, total phospholipid fatty acids, with or without acid rain. 10% PE MPs and acid rain treatment significantly increased the activity of catalase and soil CO emission. PE MPs addition did not affect the temperature sensitivity (Q) of soil CO emission regardless of acid rain. These findings suggest that MPs may interact with acid rain to affect soil ecosystems, thus underscoring the necessity to consider the interaction between MPs and ambient environmental factors when exploring the impact of MPs on the soil biodiversity and function.