Mycotoxins, secondary metabolites of fungi, are a major obstacle to the utilization of animal feed for various reasons. Wheat straw (WS) is hollow, and miscellaneous bacteria can easy attach to its surface; the secondary fermentation frequency after silage is high, and there is a risk of mycotoxin poisoning. In this study, a storage fermentation process was used to preserve and enhance fermentation quality in WS through the addition of Artemisia argyi (AA), which is an effective method to use WS resources and enhance aerobic stability. The storage fermentation of WS treated with AA had lower pH and mycotoxin (AFB1 and DON) values than the control due to rapid changes in microbial counts, especially in the 60% AA groups. Meanwhile, the addition of 60% AA improved anaerobic fermentation profiles, showing higher lactic acid contents, leading to increased efficiency of lactic acid fermentation. A background microbial dynamic study indicated that the addition of 60% AA improved the fermentation and aerobic exposure processes, decreased microbial richness, enrichedLactobacillusabundance, and reducedEnterobacterandAspergillusabundances. In conclusion, 60% AA treatment could improve the quality by increase fermentation quality and improve the aerobic stability of WS silage by enhancing the dominance of desirableLactobacillus, inhibiting the growth of undesirable microorganisms, especially fungi, and reducing the content of mycotoxins.