The promotion and application of transgenic Bt crops provides an approach for the prevention and control of target lepidopteran pests and effectively relieves the environmental pressure caused by the massive usage of chemical pesticides in fields. However, studies have shown that Bt crops will face a new risk due to a decrease in exogenous toxin content under elevated carbon dioxide (CO2) concentration, thus negatively affecting the ecological sustainability of Bt crops. Arbuscular mycorrhizal fungi (AMF) are important beneficial microorganisms that can effectively improve the nutrient status of host plants and are expected to relieve the ecological risk of Bt crops under increasing CO2 due to global climate change. In this study, the Bt maize and its parental line of non-transgenic Bt maize were selected and inoculated with a species of AMF (Funneliformis caledonium, synonyms: Glomus caledonium), in order to study the secondary defensive chemicals and yield of maize, and to explore the effects of F. caledonium inoculation on the growth, development, and reproduction of the pest Mythimna separata fed on Bt maize and non-Bt maize under ambient carbon dioxide concentration (aCO2) and elevated carbon dioxide concentration (eCO2). The results showed that eCO2 increased the AM fungal colonization, maize yield, and foliar contents of jasmonic acid (JA) and salicylic acid (SA), but decreased foliar Bt toxin content and Bt gene expression in Bt maize leaves. F. caledonium inoculation increased maize yield, foliar JA, SA contents, Bt toxin contents, and Bt gene expression in Bt maize leaves, and positively improved the growth, development, reproduction, and food utilization of the M. separata fed on non-Bt maize. However, F. caledonium inoculation was unfavorable for the fitness of M. separata fed on Bt maize, and the effect was intensified when combined with eCO2. It is indicated that F. caledonium inoculation had adverse effects on the production of non-Bt maize due to the high potential risk of population occurrence of M. separata, while it was just the opposite for Bt maize. Therefore, this study confirms that the AMF can increase the yield and promote the expression levels of its endogenous (JA, SA) and exogenous (Bt toxin) secondary defense substances of Bt maize under eCO2, and finally can enhance the insect resistance capacity of Bt crops, which will help ensure the sustainable utilization and safety of Bt crops under climate change.