Ammonia is a common and major pollutant in aquatic systems. Excessive ammonia has toxic effects on hepatopancreas in aquatic animals. In this study, we investigated the toxic effects of acute ammonia (concentration: 10 mg/L; test duration: 48 h) stress on the hepatopancreas of a freshwater mollusk, Solenaia oleivora. Transcriptome analysis identified 3355 differentially expressed genes (DEGs), including 1432 up-regulated and 1923 down-regulated genes. Many DEGs were associated with immune and stress responses, including heat shock proteins, pattern recognition receptors, and lysozyme. In addition, some DEGs were related to ammonia transport and detoxification, such as aquaporins, K+channel, V-ATPase, cytochrome p450, glutathione transferase, and glutamine synthetase. Physiological analysis showed that ammonia stress increased the activities of antioxidant enzymes (superoxide dismutase and catalase) and non-specific immune enzymes (acid phosphatase) and the levels of liver injury markers (malonaldehyde, aspartate aminotransferase, and alanine transaminase). TdT-mediated dUTP nick-end labeling assay revealed that ammonia stress induced apoptosis in the hepatopancreas. These results indicated the toxic effects of ammonia on hepatopancreas in the immune response, oxidative stress, ammonia transport and detoxification of S. oleivora. Our findings will accumulate data on the toxic effects of ammonia on the hepatopancreas of aquatic animals.