<p>Natural carboxylic acid compounds are important secondary metabolites derived from plants. They exhibit a range of beneficial effects. This study investigated the effects of natural carboxylic acids on common pathogenic fungi, specifically <i>Sclerotium rolfsii</i>, <i>Fusarium oxysporum</i>, <i>Fusarium solani</i>, and <i>Aspergillus flavus,</i> during the growth and storage of peanuts. The in vitro activity of fifteen natural carboxylic acids against <i>S. rolfsii</i> revealed that salicylic acid (EC₅₀: 25.32 mg L⁻¹), benzoic acid (EC₅₀: 61.58 mg L⁻¹), cinnamic acid (EC₅₀: 54.57 mg L⁻¹), and ferulic acid (EC₅₀: 88.70 mg L⁻¹) exhibited notable antifungal activities. Biological activity experiments indicated that benzoic acid had significant protective effects at a concentration of 200 mg L⁻¹, with 56.81% efficacy at 5 days and 59.88% efficacy at 7 days. Cinnamic acid displayed curative effects at the same concentration, with 39.12% efficacy at 5 days and 42.29% efficacy at 7 days against <i>S. rolfsii</i>. Field tests revealed that treatment with salicylic acid achieved a control efficacy of 84.67%, which surpassed that of the commercial fungicide Polyoxin (60.40%). Moreover, these four natural carboxylic acids effectively inhibited aflatoxin synthesis in peanut seeds. While, exhibiting low toxicity to nontargeted human lo2 cells. These four carboxylic acids affect the structure and function of cell membranes in <i>S. rolfsii</i> and significantly increased the activities of four defense enzymes in peanut plants. These findings suggest the potential application of these natural carboxylic acids in preventing and controlling diseases during both the growth and storage periods of peanuts.</p>