Lateral flow immunochromatographic assay (LFIA) has been widely used in the point-of-care testing field with fast results readout and portability. Nanozymes-based LFIA strengthened the colorimetric signals of LFIA strips by catalytic oxidation of the colorless substrates into colored substrates, without additional measuring equipment. But the limited specific surface area and functionalized sites of the zero-dimensional and two-dimensional nanozymes restricted their peroxidase-like activity, and the detection sensitivity cannot meet the demand for early diagnosis. Herein, a novel three-dimensional (3D) magnetic multi-metallic nanozyme with excellent superparamagnetism and peroxidase-like activity was developed as a catalytic amplification sensor for the detection of Influenza A (Flu A) viruses. Notably, two-dimensional MoS2 nanosheets with a large surface area were taken as the substrates, which can load abundant magnetic nanoparticles and peroxidase-like nanoparticles (Au@Pt nanoflowers), providing magnetic separation capability and amplifying catalytic activity. Additionally, three metals (Pt, Au, and Ag) contained in these nanozymes further enhanced catalytic performance due to LSPR and the interaction of Pt/Au and Pt/Ag. Based on a magnetic separation and catalytic amplification system, 3D magnetic multi-metallic nanozymes-based LFIA can detect Flu A as low as 0.8 pg/mL within 26 min, 125 times lower than commercial colloidal gold-based LFIA. Moreover, 20 clinical samples infected with Flu A were detected with an accuracy of 100%, and the sensitivity of inactive Flu A viruses was 140 copies/mL. This trifunctional LFIA integrates magnetic separation, colorimetric analysis, and catalytic amplification, exhibiting great potential in a pretreatment- and equipment-free diagnostic method for rapid and accurate diagnosis of Flu A.