Deterioration and mildewing caused by moisture of wheat seeds are serious problems that should be addressed for safe storage. In this work, simulated storage facilities were employed to preserve wheat seeds with different moisture contents (16%, 18%, 20% and 22%). The temperature changes in grain bulk, the mildewing situation, and the biochemical properties of wheat seeds were analyzed. Microstructures of endosperm and embryos were observed under electron microscopy. The results showed that with the increase of moisture content in wheat seeds, the deterioration and mildewing became serious. In the storage of wheat seeds with high moisture content, serious damage to the internal structure of endosperm and embryo was observed. Besides, the temperature increase and the fungal growth in grain bulk are attributed to the moisture of wheat seeds. Particularly, with the nutrient loss and cell damage, germination efficiency decreased with the extension of the storage period and the biochemical properties of wheat seeds are negatively impacted. Based on the results of this study, to prevent the deterioration and mildewing of wheat seeds and protect the biochemical properties in long-term storage, moisture should be controlled during the storage.