Plant iron (Fe) deficiency is widely present in alkaline calcium soils worldwide, and endophytes show great potential for promoting plant nutrient absorption. However, the underlying mechanisms remain unclear. To clarify the mechanisms by which the endophytic fungus Phomopsis liquidambaris promotes peanut Fe absorption, we designed this study to detect the physiological changes in peanut with P. liquidambaris infection. We measured ethylene and auxin in peanuts under Fe deficiency and found that fungal colonization promoted their accumulation (50% and 20%, respectively, at the top point). Moreover, plant Fe absorption ability and transfer were enhanced according to qPCR and enzyme results; the Fe content in the leaf increased (29.52%) as the symptoms of leaf chlorosis were ameliorated. Finally, the chlorophyll content increased (29%), and plant growth was enhanced (13.3%). We also proved that during Fe insufficiency, auxin functions downstream of ethylene to induce the upregulation of Fe absorption-related gene and enzyme activity including that of AHA4, IRT1, H + -ATPase, and FCR. We conclude that the addition of P. liquidambaris activates the auxin signaling pathway downstream of ethylene and improves peanut Fe absorption by promoting rhizosphere acidification, increasing FCR and IRT1 expression in peanut roots, leading to plant Fe absorption and growth.