Silage, especially whole crop corn silage (WCCS), is an important part of ruminant diets, with its high moisture content and rich nutrient content, which can easily cause contamination by mold and their toxins, posing a great threat to ruminant production, food safety and human health. The objective of this study was to examine effects of lactic acid bacteria (LAB) Lactiplantibacillus (L.) plantarum subsp. plantarum ZA3 and Artemisia argyi (AA) on the fermentation characteristics, microbial community and mycotoxin of WCCS during 60 days (d) ensiling and subsequent 7 d aerobic exposure. The results showed that WCCS treated with LAB and AA both had lower pH value and ammonia nitrogen (NH3-N) contents, and higher lactic and acetic acids concentration compared with other groups after 60 d ensiling. In addition, for microbial communities, Acetobacter and Enterobacter were inhibited in all AA group, while higher abundance of Lactobacilli was maintained; besides, Candida, Pichia and Kazachstania abundances were decreased in both 6% and 12% AA groups. The content of five kinds of mycotoxins were all significantly lower after 7 d of aerobic exposure. As for the total flavonoid (TF), which is significantly higher in all AA treated groups, it was positively correlated with Paenibacillus, Weissella and Lactobacilli, and negatively with Acetobacter, Enterobacteria, Kazachstania and Pichia.