The use of nanometal oxides in nanoagronomy has garnered considerable attention due to their excellent antifungal and plant growth promotion properties. Hybrid nanometal oxides, which combine the strengths of individual nanomaterials, have emerged as a promising class of materials. In this study, nanomagnesium oxide (n-MgO) and hybrid magnetic nanomagnesium oxide (m/n-MgO) were successfully synthesized via the ultrasound-mediated sol-gel method. Characterization results, including TGA, XRD, VSM, and FTIR, confirmed the successful synthesis of m/n-MgO. Both n-MgO and m/n-MgO underwent antifungal assays and plant growth promotion ability studies, benchmarked against the conventional fungicide-copper oxychloride. This study bridges a significant gap by simultaneously reporting the antifungal properties of both n-MgO and m/n-MgO and their impact on plant growth. The disc diffusion assay suggested that the antifungal activity of n-MgO and m/n-MgO against F. oxysporum was inversely related to the particle size. Notably, n-MgO exhibited superior antifungal performance (lower minimum inhibitory concentration (MIC)) and sustained efficacy compared with m/n-MgO, owing to distinct antifungal mechanisms. Nanorod-shaped MgO, with a smaller size (8.24 ± 5.61 nm) and higher aspect ratio, allowed them to penetrate the fungal cell wall and cause intercellular damage. In contrast, cubical m/n-MgO, with a larger size (20.95 ± 9.99 nm) and lower aspect ratio, accumulate on the fungal cell wall surface, disrupting the wall integrity, albeit less effectively against F. oxysporum. Moreover, in plant growth promotion studies, m/n-MgO-treated samples exhibited a 15.7% stronger promotion effect compared to n-MgO at their respective MICs. In addition, both n-MgO and m/n-MgO outperformed copper oxychloride in terms of antifungal and plant growth promoting activities. Thus, m/n-MgO presents a promising alternative to conventional copper-based fungicides, offering dual functionality as a fungicide and plant growth promoter, while the study also delves into the antifungal mechanisms at the intracellular level, enhancing its novelty.